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Get started with a free 30 day free trial
Buy Lightning Payroll
Packages starting from $199
Buy Lightning Payroll.
Packages starting from $199

How Can Restoring A Backup Delete Pay Data?

By default, Lightning Payroll opens up to look like it did when it was last closed down. If you share data between two computers (as each subscription allows) you will need to be responsible with managing your data's continuity. If your colleague does some work and you fail to restore their data before continuing, it may get lost. Please see below for a demonstration of how this problem may arise.

How Not To Backup Across Two Computers

How Can I Backup My Lightning Payroll Data?

Since Lightning Payroll is a desktop application, the data is safely stored in your own computer. We recommend you make yourself familiar with the backup features in the program.

Online backups are a great way to store an off-site, secure backup of your payroll information, with us. It is also the easiest way to pass data between two Lightning Payroll systems sharing the same subscription.

To create a backup file, click Tools >> Create backup. This saves an entire copy of your payroll data (for all companies) into one compressed file (.LPB file extension). These files can then be restored via Tools >> Restore backup.

Lightning Payroll can also make regular automatic backups to a designated folder under Settings >> Backups >> Backup your data automatically.

We recommend that you regularly place a backup on an external memory device in case your local hard drive fails.

Why Is The Program Freezing When I Restore A Backup?

If your program is freezing when restoring backups this may be due to an invalid auto-backup location. Please try the following:

Go to Settings >> Backups and either untick the box to automatically backup your data to the computer or manually set the directory to a valid location, then save the setting.

Then try restoring the backup file which was causing the freeze. If the problem persists please contact our support team.

What If I Have Trouble Viewing This Support Page?

If you are having trouble viewing these FAQs, please try the following tips:

  • Opening this webpage using a newer version of Chrome or Firefox.
  • Enabling Javascript - See here to learn how.
  • Entering the topic or question you need help with into the LP Virtual Assistant at the bottom of this page.

How Can I Set Up Online Backups?

Lightning Payroll has a built-in Online Backups feature which provides a way for you to easily save your important payroll data to the cloud. These online backups are encrypted and saved securely on our servers. In emergency situations this feature can help you to retrieve your data through your subscription.

Note: You will need a reliable internet connection, an active Lightning Payroll subscription and to have registered for this service for the feature to work correctly. See below for more information. This additional online backup service can be misused and needs to be used responsibly. We offer this as a handy extra feature and cannot guarantee the data will always be available, nor accept liability for user error or loss of your data. For this reason it is always a good idea to manage your backups yourself in addition to using this online backup feature. Please see this FAQ for more info.

To setup automatic online backups go to Tools >> Online Backups.

If you haven't yet set up online backups you will be asked to Register and create a password before you can continue. Passwords need to be at least eight characters in length, and for security reasons this password is not the same as your website and/or password application.

If you have already registered and need to connect another computer to your existing online backups you will be asked to Login and enter your password. If you have have forgotten your password, the Login screen contains a Forgotten Password area which can email through a password reset code to your nominated email address.

Once you're logged in to your Online Backups you can send a backup to our secure server to save the data currently in your program, or you can restore a previously created backup file to continue working on it. The Computer ID field is where you can add a description of the computer you're working on, or a description of the backup file you're creating. The image below shows how backups might be shared between an office computer and a laptop which share the same Lightning Payroll subscription. Only click Restore Backup if you wish to 'wind back the clock' and restore Lightning Payroll's data to an earlier point in time.

We recommend you tick the box to Automatically Backup. Also, do not click Logout unless you wish to disable the online backups. Just click Close.

Note: There is a FIVE backup limit for each active Lightning Payroll subscription. Once the limit has been reached, any new backups will automatically overwrite the oldest existing backup.

Why Can't I Restore a Backup File?

Usually a backup (.lpb) file can be restored under the Tools menu of Lightning Payroll. If the Restore Backup option is greyed out or unavailable then you are on a trial licence. This option is only available to users on a paid subscription to the software.

If you only want to restore the backup to view old data you can put Lightning into a read-only (unlicenced) mode. You will not be able to make any changes in this mode, but backups can be restored.

To switch from trial mode to unlicenced mode you need to delete the trial licence manually while the application is closed down. This file is located in the following location depending on your OS.

Windows: C:/Users/Your User's Folder/AppData/Roaming/LightningPayroll/licence.txt

Mac: ~/.LightningPayroll/licence.txt

End of Year via EMPDUPE

Submitting end of year using the EMPDUPE method.

Using the ATO’s Online Services for Business by submitting an EMPDUPE/ECI file.

Here's a tutorial video demonstrating how to generate an EMPDUPE file using Lightning Payroll's End of Year assistant.

How Do I Process EOFY and Lodge With the ATO?

Currently, the ATO allows the following methods of lodgment for your annual PAYG payroll activity. You must lodge the report by July 31st if using STP. The ATO's EOFY lodgement options are:

  • Online via Lightning Payroll using Single Touch Payroll (This is the recommended method and is available on either Windows or Mac. Requires an ATO Machine Credential). Click here to learn more about this method.
  • Online via the ATO Online Services for Business website using an EMPDUPE file (Available on either Windows or Mac. Requires a MyGovID). Click here to learn more about this method.
  • Process manually via paper/post. Only accepted on the official ATO stationary/forms. Lightning Payroll's printed payment summaries are only suitable for giving to your staff. Click here to learn more about this method.

Please select from one of the above options by entering a keyword.

Why Don't My Report Amounts Match My STP Submission?

You may notice that some amounts in the STP reports (Submission Report and Payment Summary Report), or PAYG payment summaries do not match gross totals in the Group Tax or Pay Summary Reports. This is likely due to one of the following reasons:

  • All reported amounts in STP and PAYG payment summaries are to be in whole dollars. Cents are dropped (not rounded up) when reporting to the ATO.
  • Itemised allowances (such as JobKeeper) get 'split up', and are reported separately to general gross amounts.
  • Employee Termination Payments (such as redundancy payments and wages in lieu of notice) are also shown separately.
  • Please ensure you are running your comparison reports by processed date from 1/7/XXXX to 30/6/XXXX as STP/YTD amounts are gathered using these parameters by default.

    Use Processed Date Selected

  • Ensure your pay runs are marked with the correct processed date (date of payment), as the FY should only include pays made within those dates.

    Wrong Processed Date

    Use the Set Processed/Paid Date For Pay Run tool at the bottom of the Pays screen to quickly correct any mistakes in the processed date. For more info on how Lightning manages pay dates see our FAQ here.

    Set Processed Date Button

How Can I Enter an Additional RESC/Super amount for EOFY?

If you need to make a one-off topup of RESC super for the end of financial year, this can be done two different ways. The difference being whether you are ready to pay the rest of June's compulsory super  for those same employees, at the same time.

Method (A) - Paying all of June's super (guarantee and RESC together) before EOFY
Method (B) - Paying RESC only, before EOFY, and leave the normal super for later payment in the new financial year.

Method (A)

Simply edit the employee's last pay of the financial year under Pays >> Edit Pay/s.

Edit the super by clicking the Edit button beside the super total.

Edit Super

You can then enter additional RESC amounts by adding to the RESC amount field.

This amount will then be immediately available for payment in Super Fund Deposits and will also be reported through to the ATO in your next Single Touch Payroll lodgement.

Edit Super RESC

Method (B)

If you only want to pay the RESC before EOFY you can do it as follows:

  • Go to the final pay run within the financial year, in Pays.
  • Click Create Pays.
  • Select the employees you need to pay super for, and untick Create Full Pay? This will generate an additional, empty ($0.00) pay for the employees within the pay run for you to add RESC only to.

    Create Empty Pay

  • One-by-one, edit these empty pays, and like in the image above, click Edit beside Super and add the RESC amount.

    Edit RESC

  • If you use Lightning Payroll's Super Fund Deposits area to pay super, please continue reading, if not, you should pay the RESC amount using your usual method.
  • Using the pencil at the top of the Edit Pay window you should edit the processed date of the duplicate pay so that it differs from the processed date of the other pay for that employee. This is important due to the following step.

    Change Processed Date

    Show Processed Date

  • To pay the RESC, amount go into Super Fund Deposits and click Create Deposits. Set custom dates and aim the start and end date boxes at the edited date you entered in the previous step. Tick Use Processed Date if it is unticked. Only the RESC pays should be visible, since only they have the chosen processed date. Select all, click Create and follow the usual steps from there to Send Messages and gather payment information via the Direct Entry section.

    Create Deposit

How Can I Tell If My Employees Are STP-Finalised or Tax Ready?

Lightning Payroll has a Single Touch report to give you quick information on which employees have been marked as finalised with the ATO for a financial year under Reports >> (General) STP FInalised Employees. This report has many other functions for gathering historical STP data. The most common use is demonstrated below. Note that the tax readiness of each employee's most recent STP submission is visible, along with some basic totals for quick reference.

Note: For more detailed information on your STP submission history (including all amounts submitted) please see the Single Touch Mailbox within the Pays screen.

Tax ready report form

Tax ready report

How Do I Change Financial Year Dates?

By default, Lightning Payroll takes care of your financial year start and end dates. These default to 1/7 -30/6 each year. Whether a pay falls into one financial year or another should typically be determined by the pay's processed date. Please see our FAQ on processed dates and how they affect financial year to date figures.

If a pay is processed on June 30th (or earlier) all of its figures will fall into the older financial year.

If a pay is processed on July 1st (or later), all of its figures will appear in the newer financial year.

If you need to split or shift financial year start and end boundary dates, this can be done under Company >> Financial Years.

These dates act like fence posts which section off all pays within a period of time, rounding them up to be processed in the End of Year and Single Touch Payroll sections of Lightning Payroll.

Why Doesn't An Allowance Appear Separately On An Employee's PAYG Figures?

If an allowance an employee has been receiving throughout the financial year is not showing up in their PAYG figures as itemised, this can be amended with the following steps:

Firstly, the allowance should be marked as Itemised under Employees >> Allowances/Deductions >> Allowances.

Then, to fix the allowances in earlier pays, go to Tools on the top left hand corner of the screen and select Retrospective Tool from the dropdown.

In the new window, set the date range for which you want to adjust pays that include allowances. In this case, we have set it to cover the whole financial year.

You can then select the employee or employees whose allowances you wish to adjust. As you can see here, we will be adjusting David's allowances retrospectively so that they are correctly itemised.

On the next screen, make sure Allowances is selected from the dropdown. Below, you will be shown all the pays within the previously set date range for the selected employee/s that include allowances.

Tick the boxes on the left to select the pays individual you'd like to adjust allowances for. If you want to edit allowances for all pays, click Select All/None.

Once you have selected the pays with allowances that you wish to adjust, hit Confirm Pay Selection.

On this screen, you will be able to select the allowances to edit and view their current settings. Firstly, select the allowance you wish to adjust from the Must be filtered by description dropdown. You will then see all instances of that allowance during the date range you originally set. You can then select the ones you wish to change and click Edit.

An Add/Edit Allowance window will now open for you to make adjustments. Tick Itemised? and then click Save. Once this is completed, you will now see that the selected allowances show True in the Itemised? column.

You can complete the previous step for any other allowances that need to be adjusted. Once you're finished adjusting the required allowance, click Close on the bottom right to finish.

End of Year via SBR

Lightning Payroll no longer includes the ability to submit End of Year figures via SBR as this technology has now been replaced by Single Touch Payroll. Please see here for more information on STP and other lodgement options.

How Can I Print Payment Summaries/Group Certificates?

Normally you'd print or email payment summaries at the same time as you lodge with the ATO, but they can be accessed separately any time of the year, and as many times as you like. Lightning Payroll doesn't 'close anything off' in the End of Year section. Retrieving payment summaries (group certificates) is very similar to retrieving payslips

To do this, simply click End of Year, select your financial year (FY) and click next. You will then be prompted to select the employees you wish to view/print Payment summaries for, and follow the prompts.

Once you are looking at the Payment Summaries screen, click the Payment Summaries button and Lightning Payroll will generate your employees PAYG summaries in a printable PDF format.

How Can I Edit Payment Summaries?

If you need to make adjustments to payment summaries, click the Advanced button on the Payment Summaries screen. You can then change the values as needed.

If you wish to undo any manual adjustments made in this screen, simply click on the Refresh button.

If you have already lodged this payment summary to the ATO, and then need to resubmit your edited version make sure to tick the Amendment? box before resubmitting.

End of Year via Paper Form Submission

Submitting end of year on paper (by post)

If you would like to lodge your annual payment summary report on paper, you can do so using the ATO’s paperwork. If you haven’t received a stationary pack from the ATO and wish to submit on paper you can order a PAYG payment summary statement here.

Note: The ATO does not accept documents printed from Lightning Payroll. Lightning Payroll can provide printed payment summaries suitable for your staff however, through the Payment Summaries button in the End of Year section of the program.

Where Can I Find The Latest End Of Year Checklist?

Click here to see the latest Lightning Payroll EOFY checklist mailer. This gets emailed out to all active users each June.

What are the Different Employment States?

Employees can have different states or statuses in Lightning Payroll. These states are 'Active', 'Inactive', 'Terminated' and 'Deleted'. These are explained in detail below.

Active: an active employee is one who is currently working and being included in pays. This is the default states when you add an employee and is indicated by the 'Active pay recipient' box for that employee being ticked in Employees >> Pay Settings >> Pay Rates.

Inactive: an inactive employee has not been terminated but is not currently working or being included in pays. This is indicated by the 'Active pay recipient' box for that employee being unticked in Employees >> Pay Settings >> Pay Rates.

Terminated: a terminated employee has been officially terminated in the program. This is done during the employee's final pay in the Edit Pay screen by pressing the Terminate Employee button. Terminated employees show up in red in the Employees list when you tick the box 'show terminated employees'. Please click here for more information on terminating employees.

Deleted: A deleted employee has been completed removed from Lightning Payroll. If you delete an employee using the 'Actions' button in the Employees section, all their past and present data will be removed.

NOTE: Deleting employees is not recommended. If an employee has left your company, you should terminate them through the Pays screen instead.

What Are the System Requirements and/or Limitations of Lightning Payroll?

Compatible Operating Systems

Lightning Payroll is a desktop application compatible with Windows 7 (and above) and Mac OSX 10.12 (Sierra) and above. We only support these operating systems.

The software is not designed for or tested on server-based operating systems, nor is it able to be installed on mobile devices (E.g. IOS, Android, etc).


Minimum system requirements for using Lightning Payroll are:

  • Intel Core i5 (sixth generation or newer) or equivalent
  • 8 GB RAM
  • 500 GB internal storage drive

Screen/Monitor Size

Lightning Payroll is not recommended for screen sizes below 15 inches as some screens will be squished or very hard to use.

For ultra hi-res and 4k monitors you may need to configure these for clarity in the program.

Pay Run Schedules

Lightning Payroll accomodates the following pay schedules:

  • Weekly
  • Fortnightly
  • Monthly

You can use any combination of these three pay schedules on any of the business entities within the software, however only one schedule of a type per company is possible (I.e. you cannot run two simultaneous weekly schedules ending on different days of the week).

Approved Income Streams

Lightning Payroll is certified by the ATO for the following Single Touch Payroll (Phase 2) income streams:

  • Salary and Wages
  • Working Holiday Maker
  • Closely Held Payee
  • Voluntary Agreement

Support Team Boundaries

Lightning Payroll support is free to our subscribers, however certain topics are outside of what our team may assist you with:

  • Teamviewer/Remote access - Our support team do not 'remote in' to customer's systems. This is not necessary when helping solve issues as backup sharing with support is built-in to the software.
  • Email configuration and troubleshooting - Lightning Payroll includes a basic SMTP server settings search feature under the Company >> Email tab which finds common email settings. This uses a third-party API to obtain settings. Beyond this you'd have to contact your email account provider for gaining those settings, our support team are unable to provide settings for email providers.
  • ATO machine credentials and websites - Our support team are unable to provide support for the ATO's software or websites. For ATO technical support please contact their Technical Helpdesk on 1300 139 373.

How Can I Update to the Latest Version of Lightning Payroll?

Click the Check for Updates Now? at the bottom of the program to check for any newer versions.

Reinstalling or updating your software fixes most issues if they should arise.

If updating fails for some reason, you can download the latest version directly from the links below:

(your data is safe and will not be affected by reinstallation)

Download for Windows (Windows 7 and above, assuming you have the latest Windows updates)
Download for Mac OSX (Version 10.12 and above)

If you find your auto-updates say they are working but you are being returned to the same version of the program you probably have a broken update patch on your computer. Please click here for a short guide on how to fix this issue.


How Can I Check What Version of the Software My Computer is Running?

You can check which version of the software you're using at the bottom of the Lightning Payroll program window.

You can check if your version is the most current by clicking Check for updates now? at the bottom of your program. Click here to find out more on how to update your software.

Can I Install The Program On Multiple Computers?

A Lightning Payroll subscription allows you to download the program onto two separate computers. However, the two installations do not talk to each other automatically, and do not allow simultaneous use. Keeping in mind that Lightning Payroll is a desktop based application, not an Online application.



Where Can I See a Demo of Lightning Payroll?

Here is a demonstration of how to process a pay in Lightning Payroll.
Check out more on our Youtube channel.

What Options Are Available When Emailing Employees?

Lightning Payrolls also allows you to configure additional preferences for emailing employees.

To view this options, go to Employees > Details > Email Options.

In this menu, you have the following options:

  • Alternate email: Entering another email here specifically to send payslips to
  • Email Payslips?: This tickbox lets you choose whether you want the employee to receive payslips by email or not
  • Email payment summaries: This tickbox will also allow you to email PAYG/group certificates directly to employees at the end of financial year.

Can I Purchase Lighting Payroll For Less Than A Year?

Lightning Payroll is only available as an annual subscription. There is no option for a subscription term less than one year.

Will I Lose The Data I've Entered When My Trial Expires?

As Lightning Payroll is a desktop-based application, the data you enter into your free trial will be saved on the computer you've been working on, even after your free trial expires. This means that if you decide to purchase the program after the free trial expires, you will be able to pick up where you left off and continue entering data without losing what's already been done.

The trial version of the program you've been using will be unlocked and able to be used as the full version once payment has been made and your Subscription ID is entered into said trial version.

How Can I Set Birthday Reminders?

If you would like to create a birthday reminder for an active employee go to Settings >> Reminders. Click on the box next to Birthday Reminders On, which is located at the bottom left of this screen. Select how many days notice you wish to have. Then click on Create Birthday Reminders For Active Employees.

You can edit each reminder by clicking on the pencil icon and saving those changes. When entering into Lightning Payroll, that is when you will be notified of the birthday reminder.

How Can I Import Data Into Lightning Payroll?

Lightning Payroll is not able to import data from any other software.

All data will have to be entered into the program manually.

Where Can I View Order History and Tax Invoices for Licence Payments?

You can view your licence order history, as well as print and download .pdf copies of your tax invoice/s for licence payment via our website. You will need to login to Client Login on our website, then click on My Account, then click View Your Order History. From here you can see the list of your orders under this account, and click View on the order you'd like to see.

To print or download a .pdf copy of the tax invoice for your chosen order, click on Show Tax Invoice, then select either Print This Invoice or Download A PDF Copy from the buttons on the top right-hand corner of the page.

How Can I Purchase Lightning Payroll?

To purchase an annual Lightning Payroll subscription it just involves going to the 'Buy Now' page of our website, choosing a licence to suit your needs from the options available, registering an account and making payment.

Once your payment has been confirmed you will receive an email with a subscription ID number which needs to be entered into the program when you open it for the first time.

Please Note - When using a trial version you have not yet registered an account with Lightning Payroll.

How Can I Pay For My Annual Subscription?

You can pay for your annual subscription over the phone with us, or through our website via Client Login >> My Account >> View/Renew/Upgrade Subscriptions.

You have two options for payment:

  • Using a Visa or Mastercard to make a credit card payment, which is instant; or,
  • Making a Direct Deposit payment to us through your bank account. Please not that paying by Direct Deposit means we will need to wait until the funds clear in our account before we're able to provide you with your new Subscription ID to use the program. This usually occurs by the next business day after your transfer.

How Can I Setup Leave Requests?

Before your employees can make leave requests through our online employee portal you must have activated their online portal settings under Employees >> Details >> Online Portal. The two main settings you will need for leave requests are Activate This Employee's Online Portal and Allow Employee to Create Leave Requests.

Note: Online portal settings can be configured for multiple employees simultaneously under Tools >> Multiple Employee Portal Settings.

online portal settings left

You can configure other settings as you wish, particularly the standard working days and leave request types to the right of the screen.

online portal settings right

How Do Employees View or Create Leave Requests?

Employees can login to their personal portal here and click on the Leave tab.

In the Leave section, they can view their current leave balances (if enabled within their online portal settings), along with any current or previous leave requests.

Employees can search and filter through their past leave requests using the dropdown and date boxes. They can also delete pending requests and cancel any other request if need be. Editing from an employee's perspective is limited to the adding of notes.

balances and requests section

To request leave, the employee would need to click on the Request Leave button. They will then see the following form where they can enter the start and end dates for the leave, and the type of leave they wish to take.

The Daily Duration section shows how many hours will be applied to each date within the leave request.

If the selected leave type's balance is permitted a forecast table will be shown at the bottom.

For multi-date leave requests the app will rely on the employee's Standard Working Days (default is Mon-Fri), skipping any days which are not normally worked. An employee's standard working days are configured in their Online Portal settings described above.

New leave request form

How Do I Manage and Approve Leave Requests in Lightning Payroll?

Once a leave request has been saved a notification email will be sent to the approver via the registered company email address (under Company >> Details within Lightning Payroll).

New request notification email

You will also receive a prompt when you next enter the Pays screen within Lightning Payroll.

Pending leave request prompt

Saying yes will show you the leave request management window, otherwise accessible via Pays >> Timeclock/Portal Sync >> Manage Leave Requests.

Leave Request Management

To view, edit or approve a leave request, click the edit pencil button beside the request you wish to edit. You will be able to modify dates, leave types, status and notes within any leave request.

Leave Request Approval

If you forget to change the status a reminder message will appear.

Leave Request Approval Reminder

When you change the status of a leave request, or when you add a note to a leave request, a notification email will be sent to the employee to inform them of the change.

Leave Request Employee Notification

How Do I Make A New Leave Request On An Employee's Behalf?

To add a new leave request click the green plus button in the main leave requests management window. You will then be able to press the green plus in the next window to add specific dates to the request. Keep in mind a leave request may consist of multiple leave types if necessary (E.g. Annual leave and Public Holiday) 

Leave Request New Days

Once you have added one or more days to the request you will see them listed like the following example. Notice how if the program detects any public holidays within the leave request's dates it will make a mention. If you would like to change the leave type of any dates to public holiday (or any other leave type you might need), click the edit pencil beside the date in question.

Leave Request New Days List

Any approved leave will then automatically add itself to pending pays, so long as the pay run start and end date contain the date of the approved leave request.

How Do I Pay Leave?

To process leave for an employee, go into the Pays section of the program and then click the Edit Pay button for the employee taking leave. In the Leave tab you can use the green plus button to add a new leave item, or the pencil icon to edit an existing leave entry. Simply select the type of leave you will be paying and alter the other values as necessary. The employee's ordinary time hours will be reduced by the amount of leave taken, to help prevent accidental overpayment.

Paying out leave in advance

If an employee is going on leave, and you would like to pay them for all of that leave in the one pay period, tax calculations will need to be advised within the program. This can be done at the bottom of the the main Edit Pay window by spreading the tax calculations over multiple pay periods.

For example, if you pay weekly and you intend to pay the employee for two weeks leave that they'll be taking, in addition to the week they have just worked, the amount of pay periods you would need to enter would be 3.00 .

Employee is cashing out their leave

If an employee wants to be paid out some of their annual leave, or long service leave, without actually taking it, you can tick the 'Cash out' option when entering the leave in their pay. Do NOT spread tax for leave that is being cashed out.

How Do I Enter Paid Parental Leave, Unpaid Leave or Worker's Compensation Payments?

If an employee is on paid parental leave, unpaid leave or on leave whilst receiving workers compensation, there are  paid parental, unpaid and worker's compensation leave types that can be selected when processing pays.

You can select any of these options in the Leave taken in this pay section as shown below.

Once you have selected paid parental, unpaid or workers compensation, you can set the duration and the hourly rate for the leave.

For paid parental leave and workers compensation, if you only have a daily or weekly rate, you can calculate the hourly rate by dividing the dollar figure by the number of hours the employee normally works in a day or week respectively.

For example:

If you need to pay $1000 per week and the employee typically works 38 hours per week, the hourly rate would be $1000 / 38, or $26.32.

If you need to pay $150 per day and the employee typically works 8 hours per day, the hourly rate would be $150/ 8, or $18.75.

Lightning Payroll will remember this hourly amount (since it is unlikely to match their normal hourly rate), and save it automatically under Employees >> Leave >> Advanced pro rata leave settings, for the next time they receive this special leave type.

Super and Leave Accrual Settings

Paid parental leave, unpaid leave and workers compensation may or may not attract leave accruals and superannuation depending on your state legislation or industry awards.

If you need to adjust whether leave or superannuation accrues on paid parental leave or workers compensation, you can do this under Employees >> Leave >> Advanced Pro Rata Leave Settings.

Note: If you're not able to select any of the advanced settings, it means the employee has not been set to accrue leave on a per hour paid (pro-rata) basis. You can turn this on under Employees >> Leave >> Leave Settings.

How Does Lightning Payroll Calculate Leave Accruals?

Leave accruals in Lightning Payroll can be controlled by configuring an individual employee's settings under Employees >> Leave >> Leave Settings. Accruals can be made to occur by the pay period or by the hours worked (pro rata).

Note: Lightning Payroll applies the most common accrual settings when a new employee is created, based on the given STP employment status. Leave settings should be carefully considered to suit your employee's state and award. Each state has different LSL rules and each award can have its own particular requirements such as annual leave loading or differing entitlement days per year.

Accrue by Pay Period

A typical full-time employee's settings might look like this. In this example the employee does not get annual leave loading.

This employee accrues 20 days holiday leave and 10 days sick/personal leave as per the Fair Work National Employment Standards.

How many hours per day this calculates is based on the employee's award hours for a full day. These are configured under Employees >> Pay Settings.

The formula used by Lightning Payroll to calculate accruals for one pay run in this scenario would be:

days of leave entitlements per year x award hours per day / pays per year

E.g. A weekly full-time employee would accrue:

Annual - 20 days X 7.6 hrs / 52 weeks = 2.92307 hours p/wk

Personal - 10 days X 7.6 hrs / 52 weeks = 1.46153 hours p/wk 

Long Service Leave is slightly different as it is usually required to accrue by weeks per 10 or 15 years. 

In this case it would calculate:

(8.6667 weeks p/yr X 38 hours p/wk) / 10 yrs / 52 weeks = 0.6333 hours p/wk

Accrue by Hours Paid

A typical part-timer with pro-rata annual leave accruals would look like this:

Their pro rata leave accruals are controlled based on the Hours leave accrued, for each hour paid fields.

This decimal value would accrue the same result as above if someone worked 38 hours per week.

For example:

Annual leave - 38 hrs X 0.076923 = 2.92307 hrs

Personal/Sick leave - 38 hrs X 0.0384611.46153 hrs

Long Service - 38 hrs X 0.016673 = 0.633574 hrs

How Is Leave Affected by JobKeeper?

For detailed information on accruing and taking leave when receiving JobKeeper payments please see the Fair Work Australia website. Common scenarios they reference are below.

Requesting employees to take annual leave

If an employer asks their employee to take annual leave, the employee has to consider the request. They can’t unreasonably refuse it.

Employees who are on annual leave continue to accrue their usual leave entitlements while they're on leave, and the period of leave counts as service. 

Taking annual leave at half pay

Employees who make an agreement to take annual leave at half pay continue to accrue leave entitlements (such as annual and sick and carer’s leave) as if they were taking annual leave at full pay.

If an employee takes leave at half pay, redundancy pay and payment in lieu of notice of termination are also calculated as if the agreement hadn’t been made.

Taking paid leave instead of minimum JobKeeper payment

If an employee is given a JobKeeper enabling stand down direction, the employee will be entitled to be paid at least the amount of the JobKeeper payment for a fortnight ($1500 before tax). This amount may be less than the employee would have received if they had worked their usual hours during that fortnight.

If an eligible employee has been given a JobKeeper enabling stand down direction to work less hours than usual (or no hours), but wants to be paid their normal pay, they can agree with their employer to use their paid leave entitlements to top up the amount they’re being paid. If that happens, for the time they’re on paid leave, they’re not on a JobKeeper enabling stand down.

An employee and their employer can agree for the employee to take leave (such as annual leave or long service leave), including taking annual leave at half-pay. In any relevant fortnight, the employee must be paid the greater of either the amount of the JobKeeper payment or their usual pay for work performed, including leave payments.

An employer can’t unreasonably refuse an employee’s request to take annual leave.

Employees subject to a JobKeeper enabling stand down direction still accrue their usual leave entitlements for the period the direction applies (as if the direction hadn't been given to them).

How Do I Correct or Adjust Leave Totals?

If one or more of an employee's leave balances have accrued incorrectly, or have been set up incorrectly, they can be corrected in a number of ways.

We would recommend using our new Recalculate Leave on Pays Tool which can be found in the Tools menu on the top left of Lightning Payroll.

This tool gives you the ability to retroactively apply an employee's corrected leave settings to old pays. Please ensure you have reviewed and/or corrected their leave settings under Employees >> Leave >> Leave Settings prior to using the tool.

This tool allows you to recalculate leave for an employee and automatically set the new balances.

In the following example, David Cattermole's leave has not been calculating correctly since the beginning of January.

As leave is calculated on a per pay basis, the first thing we will do when using the tool is to select the date range for the pays we wish to recalculate leave on. In this case, we have chosen the 1st of January up until the 6th of February (the end date of the most recently completed pay run).

Once we've set the dates, we can proceed to the next screen and select David from the list as we wish to recalculate his leave.

The next screen will show us the pays for David within the date range we set. We wish to recalculate leave on all the pays for the entire date range so we will select all (you will typically want to select all pays in most scenarios).

The next window will ask us to select the leave type we wish to recalculate for David. In this example, we want to recalculate his holiday, sick and long service leave as we think they all may be incorrect for the period.

The final page will display the leave recalculations for David. As you can see in the green square, the tool is displaying David's current holiday accrual in the left column and the recalculated accrual in green in the right column.

The blue underline shows that for the pay ending the 6th of February, David's holiday accrual was correct as it matches the recalculated accrual.

You can generate a printable report by clicking the Print/Preview button on the bottom left. To apply the recalculated amounts, simple click the Finish button on the bottom right.

Alternative methods for adjusting leave balances

Leave balances as at the most recent completed pay can be amended under Employees >> Leave >> Leave Entitlement Adjustments. If you know the correct balance already, simply overwrite the incorrect balance with the correct one.

If the total you wish to enter is from another period of time than the most recent completed pay, you can go to Pays >> Last Pay Run >> Edit Pay >> Edit Leave Balances and adjust the balance from whichever period you like.

If you don’t know the total and need to recalculate, you can use Lightning Payroll's leave calculators, seen to the right-hand side of the Leave Entitlement Adjustments screen. Alternatively, you can also utilise Fairwork's online leave calculator here.

How Do I Enter Existing Leave Balances?

If you are new to Lightning Payroll and setting up an employee with existing leave balances, you can enter your these amounts in their first pay. Once you have gone into the Edit Pay screen for an employee, you will see the Leave Balances Edit button on the left hand side of the screen. Here is where you will be able to enter your initial balances. Previous amounts need to be added to the system generated accruals from the current pay run.

For example:

Let's say that the employee’s leave balance on their most recent payslip shows 45 hours and 30 minutes of annual leave (45.5 hours). When you click Edit Pay >> Edit Leave Balances you will notice a small amount of leave has accrued. For example, our employee works 38 hours a week, and so they will accrue 2 hours and 55 minutes of annual leave (2.92 hours). You will need to add this amount to their leave balance as of last week. So for this example we would add 2 hours and 55 minutes to our original balance of 45 hours and 30 minutes, which will result in a total 48 hours and 25 minutes (48.42 hours). This is the updated leave balance as at the end of their first pay period inside of Lightning Payroll.

How Do I Add Additional or Custom Leave Types?

You can set up custom leave types in the program for things like RDOs, Time in Lieu, and Bereavement Leave by going to Company >> Leave Balance >> Create Leave Balance and creating the leave type here. Once the leave type exists in this area, you will need to go to Employees >> Leave >> Leave Accruals and use the green plus symbol to add the recently created leave type to each employee who requires it.

What Is The Difference Between Full Paid Licence, Trial Licence and Read-Only (Unlicenced) Modes?

Lightning Payroll can operate in three different licensing modes. The diagram below gives an idea of how the three modes work.

To find out how to renew, or upgrade your subscription click here.

How Can I Remove My Subscription From Existing Lightning Payroll Installations So That It Can Be Installed On A New Computer?

Any annual Lightning Payroll subscription allows you to unlock and use the program on two computers at any one time.

If Lightning Payroll is giving you either of the following errors you will need to clear one or both of your two allowed seats from the current licence/subscription.

Older Versions Max-Seats-Error

Old registered seats exceeded error

Newer Versions Max-Seats-Error

New registered seats exceeded error

Note: Removing the licence from Lightning Payroll does not affect your pay data or your program installation at all. It will simply lock your application soon after removal, putting Lightning Payroll into a read only state until an active licence is again provided.

There are three ways to fix this error:

  1. Removing the installed licence from an existing Lightning Payroll installation at the top of the program under Tools >> Licence Details >> Remove System. Remove system button
  2. Sometimes the old system has crashed and you cannot open the program. In this case you should log into your client account here on our website and go into your subscriptions. Here you can release the seats for any of your subscriptions. This will free up both seats of your subscription for you to then reenter as needed. My subscriptionsRelease seats
  3. Contact our support team and we can reset your seats for you.

How Can I Check When My Subscription Expires?

When your annual subscription is within 60 days from expiration Lightning Payroll will remind you whenever you open the program. We don't automatically invoice our users.

To manually check the expiration date on your Lightning Payroll subscription or to view your other subscription details, open the program and click Tools >> Licence Details.

To find out how to renew, or upgrade your subscription to allow more employees click here.

You can also view your subscription expiry information by logging into your account under Client Login on the top right of our website.

Why is the Trial Version Asking for Licence Details?

If you have downloaded the free trial and you are being prompted enter licence details, it is likely you have already used the trial previously on the same computer.

The trial lasts for 30 days from the first time you run the trial version. If your trial has now expired, we also offer a 30 day money back guarantee for first time subscribers to Lightning Payroll.

However, if you are certain you have never used the trial before but it is still asking you to enter details, please contact our support team.

I Have Paid For My Licence What Happens Next?

Once you have paid for your annual subscription you will receive an Invoice through to your registered email address with a new subscription ID.

To enter the new subscription details into Lightning Payroll go to Tools >> Licence Assistant >> Enter Registered Email Address >> Subscription ID >> Download Licence >> Install.

Once the Install diaglox box disappears you have successfully installed the new licence.


Why Is Lightning Payroll Asking Me For My Licence Details?

After opening Lightning Payroll, you may occasionally be prompted to enter your licence details. This will occur if your subscription has expired, but it can also occur from time to time for security reasons, and to ensure that you're running the latest version of Lightning Payroll.

If this occurs, please enter your registered email address and subscription ID number. Your subscription ID is always a six-digit number. This number gets emailed through when you renew your subscription each year, and it can also be seen by logging in to your account here on our web page (shown below).

If you are unable to login, you can reset your password here.

Licence Errors

If you encounter a Signature Invalid for Licence error (shown below) when entering your licence details, please see here.

If you encounter an error saying The number of registered systems has reached the maximum allowed by this licence (shown below) then your subscription ID has already been used on two separate computers since renewal.

You'll need to remove your licence from one of the two other computers under Tools >> Licence Details >> Remove System before it can be re-used once again.

If you encounter a Local Licence Install screen (shown below) when entering your licence it may mean that you're on an older version of Lightning Payroll. Click here for help updating Lightning Payroll to the latest version.

It can also mean that Lightning Payroll is unable to connect to the internet. Please check your internet connection, and if that fails try disabling third-party antivirus/firewall software, as they may need to have an exception created.

How Can I Renew, or Upgrade My Subscription?

To renew your annual subscription, you will first need to login using your email and account password. If you are unable to login, you should reset your password.

Once you have logged in to the My Account section, simply click View/Renew/Upgrade Subscriptions.

Signature Invalid For Licence Error

If you are getting a Signature Invalid For Licence error when trying to enter your licence details, this means one of two things:

  • Your subscription has expired and you will need to renew your licence to continue using the program as normal; or,
  • Occasionally, we have to get everyone to update beyond a particular version of the program. We do this by making the Online Licence Install box pop up upon opening the program, requesting you enter your registered email and subscription ID; when these details are entered, you will get a Signature Invalid For Licence Error. At this point, if you know your licence is not expired, you should click Cancel to the Online Licence Install and then click on the Check For Updates Now button in green writing on the bottom toolbar of Lightning Payroll. Once updated to the latest version, the program will ask for your licence details once more, at which point you can enter them again, and they will be accepted.

I've Forgotten my Password for Online Backups

If you cannot remember your password to login to the online backups portal, you can reset it by clicking Forgotten Password.

A reset code will be sent to your registered email address. You can then choose a new password, confirm the new password and input the reset code you will have received by email from Lightning Payroll.

Reset or Remove Application Password

If you would like to reset or remove the application password for Lightning Payroll, you can do this under Settings.

To reset the password, go to Settings > Password and enter and confirm the new password you wish to use.

To remove the existing application password, click Remove Application Password on the bottom right.

If you cannot get into your program at all, you will need to contact our support team for assistance.

Why Can't I Login to this Website?

If you are a current paid subscriber to Lightning Payroll you can log in to your account at the client login link at the top of this page. If you have forgotten your password, please reset it here.

If you are a trial user you will not yet have an online account. You can sign up as a new user after selecting the appropriate subscription package here on our purchase page.

How Can I Terminate an Employee (Basic)?

For a detailed termination, please see our FAQ here.

To terminate an employee, go to Pays >> Edit Pay and click the Terminate Employee button (above the Save + Next button) on the bottom-right of the screen when editing the employee’s final pay. This will bring up the employee termination assistant.

Here, you will be prompted to enter the termination date, the reason for termination, and then on the next page, you will be able to select which leave types need to be paid out. If no leave is to be paid out, you will be able to deselect them all.

If you need to enter in wages in lieu of notice, you will be able to do this on the following screen. Otherwise, you can hit Next to continue, and you will be brought to a final termination summary screen. If you’re happy with the termination, you can then click Finish, then Save and Close on the pay.

How Can I Terminate an Employee (Detailed)?

For a basic termination, please see our FAQ here.

The first screen of the termination assistant will ask you to enter the termination date and select a a reason for termination. With the exception of a genuine redundancy or other listed circumstances, ordinary termination is typically the appropriate option.

If you select genuine redundancy, you will be prompted to enter the payout amount for the redundancy payout amount on this screen. Please see the ATO's page here for more information on redundancy payouts.

The next screen will ask you to select non-ETP payout options. This is where you can select or deselect which leave types you need to pay out to the employee as part of their termination. Lightning will calculate the appropriate payout amount for the selected leave types based on the employee's hourly rate (and their leave loading rate if applicable) and the current leave balance in hours and minutes.

You can also pay out additional non-ETP amounts on this screen. Please see the ATO's page here for more information on non-ETP payment types.

The next screen is where you can enter ETP payout options. A common example of this is paying out wages in lieu of notice. If you don't need to pay wages in lieu of notice, you can skip this screen by clicking Next.

Otherwise, there are a number of ways to payout wages in lieu of notice. The most common way is to select the Number of Hours Notice option. As shown in the example below, the employee is being paid out four weeks of wages in lieu of notice. In this example, fours week is equivalent to 152 hours (based on a 38 hour week), although the amount can vary based on the relevant contract or award.

Along with the option to also pay out unused sick leave if required, there is an advanced settings option. Selecting this before clicking Next will take you to the advanced settings screen.

The advanced settings screen is useful to view and edit the current lump sum leave balances being paid out if needed prior to completing the termination.

Additionally, when clicking Next, you will be taken to a further screen where you can view ETP codes and edit ETP tax amounts if required. This can be particularly helpful when processing genuine redundancies.

The final screen will show you the termination summary. This shows you any and all amounts being paid out along with the types of payouts. At this point, if you're happy with the termination amounts, you can click Finish to complete the termination.

If you want to generate a report of the termination you've just completed, click on the Preview button

How To Setup A Deduction?

To setup a deduction for an employee go to the Employees tab >> Select the Employee on the left hand side >> Click on Allowances & Deductions >> Deductions >> Click on the green plus symbol to add the deduction & Save.

This deduction can then be seen in the Pays tab >> Edit Pay for this employee >> Click on Allowances/Deductions >> Deductions. You can edit the amount manually by clicking on the pencil icon.

A common type of deduction is a child support payment. If you mark a deduction as a child support payment it will check the minimum protected earnings amount against the net before allowing you to save the pay. These protected earnings amounts are updated each January.

You can also link a deduction to a secondary bank account for an employee (entered under Employees >> Details >> Bank Accounts). This would then include the deduction in an additional line entry within the direct entry banking file. If you are linking a deduction to a bank account, you will likely not need an amount entered against the account itself, under Employees >> Details >> Bank Accounts.

Note: If the deduction is required in a past completed pay, you will have to unlock that pay by clicking on the padlock in the bottom left hand corner. Then click on Allowances/Deductions >> Click on the green plus symbol under Deductions & Save.


Which Reports Show JobKeeper Amounts?

The best way to gather JobKeeper payment information is via two different Lightning Payroll reports. They are:

  • Allowances Report - This can show specific information on any JOBKEEPER-TOPUP allowances. These topup allowances should have been used on pays where JobKeeper employees where paid ABOVE their worked earnings.

    Allowance Report Form

  • Pay Run Report - The Pay Run report includes a TOTAL JobKeeper amount in the JK Eligible? column. This is inclusive of any topup amounts described above.

    JK amounts pay run report

How Can I Show Casual Loading On A Pay Rate?

For certain casual employees it may be necessary to display their base pay rate and their casual loading amounts within pays and payslips. This can be easily handled via a custom pay rate's description. Customised, secondary pay rates are added under Employees >> Pay Settings >> Special User Defined Pay Rates.

In the below example you can see the $25 hourly Saturday pay rate's breakdown being shown in the description field.

Casual loading

How Does Lightning Payroll Handle YTD Figures And Pay Processing Dates?

Prior to Lightning Payroll version 2021.5.0, when it came to applying a tax scale or assigning a financial year to a pay, the program was designed to use the pay period's end date over the pay's processing date. We have updated this to simplify and automate YTD calculations used for Single Touch Payroll so that less errors and headaches would occur at EOFY. The processed date for a pay refers to the date when payment is made to an employee.

Why Is The Pay Processed Date Important?

The date of payment is important to Fair Work Australia as it must be included on every payslip, however its main importance relates to the ATO with tax and YTD calculations. The ATO states that a financial year's payments are not about what pay runs end between July 1 and June 30, but what payments are made or processed within those dates.

From the ATO:

"If salary and wages are accrued in the current financial year (prior to 30 June) but paid in the following financial year (on or after 1 July), the full amount of the payment will be taxed at the following financial year's tax rates and included in the following financial year's payment summary."

Older versions of Lightning Payroll required that financial year boundary dates be stretched or contracted so that the pays processed would be attributed to the right financial year. This is now automatic and rests solely on the processed date of pays entered into the program, so please be mindful of how processed dates work (see below) and that they are accurate.

How Are Pay Processed Dates Set In Lightning Payroll?

Pays Processed Date Column

Pay processed dates are most prominent in the centre of the main Pays screen table (above), and they are controlled in a number of ways within the software:

  1. Automatically, when completing/saving a pay: The date that you first process and save a pay sets the initial processed date of the pay. In other words, when the pay changes status from Pending to Completed.
  2. Automatically, when creating a direct entry payment file: The processing date used in a direct entry file will automatically update the processed date of all pays included within the file.

    Direct Entry Processed Date

  3. Manually, for a single pay: You can edit an individual pay's processed date using the pencil button at the top of the Edit Pay window.

    Edit Processed Date

  4. Manually, for multiple pays in a pay run: You can edit the processed date for an entire pay run at the bottom of the main Pays screen, using the Set Processed/Paid Date For Pay Run button. Just enter the new processed date, and select the pays you wish to change the date for and click OK.

    Set Processed Date Button

    Set Processed Date Dialog

What If I Prefer The Old Pay Run Date Program Behaviour?

If you would like the program to operate as it used to, using pay run end dates to collect YTD amounts used for STP and payment summaries, you may. Just go into Settings >> Display/Time Settings and untick the box which says Use pay processed dates for calculating YTD figures?.

Processed Date For YTD Setting

Do Reports Use Processed Date Or Paid Date?

When running reports in the software you will often get the choice between selecting pay info based on pay run end date or processed date. Simply tick to Use Processed Date or untick to go by pay run end date when in the report form. Lightning Payroll will remember your preference for each report individually.

Processed Date For Reports

Can Financial Year Dates Be Edited?

If you would like to edit financial year boundary dates (to further control which financial year captures which pays) you can do so under Company >> Financial Years. See our FAQ on the topic for more information.


How Do I Setup A Salary Sacrifice?

To add a Salary Sacrifice for an Employee you will find this under the Employees tab. Select the employee to the left of the screen. Click on Pay Settings >> Salary/Wage Sacrifice and click on the green plus symbol to add in the sacrifice & Save

If this is to be a Salary Sacrifice as Super, ensure you tick the Is Super/RESC? tickbox, and attach the employee's super fund to the sacrifice.

Where Do I Enter a Back Payment?

If you need to make a back payment to an employee, this can be done as follows.

Simply edit the appropriate pay run for the employee under Pays, then click Edit Pay/s.

Enter a back payment by clicking the Edit button beside Back Payment.

Edit Backpayments

You can then enter a description and select a tax method from the available ATO options. The date fields are only enabled when relevant.

Edit Backpayment Amount

Where Can I Enter a Bonus or Other Irregular Gross Payment?

If you need to make a bonus or other miscellaneous gross payment to an employee, this can be done as follows.

Simply edit the appropriate pay run for the employee under Pays, then click Edit Pay/s.

Enter a bonus or other gross payment by clicking the Edit button beside Bonus/Commission.

Edit Bonus

You can then enter a description and select a tax method from the available ATO options. The date fields are only enabled when relevant.
If you would like to change the description, you first need to create a new item for the employee under Employees >> Allowances/Deductions >> Bonuses.

Edit Bonus Amount

How to Enter WorkCover Payments

If an employee needs to receive WorkCover payments, you can set this up as a custom pay rate under Employees >> Pay Settings >> Special User Defined Pay Rates.

Click on the green plus button to add a new custom pay rate. For the description, enter a name for the pay rate (e.g. WorkCover).

Then, click the Rate Type dropdown and select Special. You can then specify a dollar amount for the pay rate below. Enter the pay rate specified for the employee's WorkCover. This will typically be a daily or weekly. You can enter the figure and then change the Units option from Hours to Days or Weeks as you prefer.

If you need to prevent super from being calculated on on this pay rate, tick the Overtime? box. Finally, click Save.

If you need to turn off leave accruals during this time, you can disable leave under Employees >> Leave >> Leave Settings.

You will now be able to select this pay rate when processing pays for the employee. If you have disabled leave, set a reminder (under Settings) to enable it again once the employee returns to work.

How Do I Print and/or Email Payslips?

Printing and/or emailing paylips is done from the Pays tab of the program. Once a pay has been saved to a Completed status, you're able to print a payslip for that particular pay by clicking on Payslips >> This Pay Run and ensuring either Print payslips or Print and email payslips is selected at the bottom of the box, before clicking Next. Select the employees you'd like to print a payslip for and click Next, then select Preview/Print Payslip; you can now print the payslip/s by clicking on the printer icon on the top left of the preview. You can also save the payslip as a .PDF by clicking on the red floppy disc icon next to the printer icon at the top left of screen.

You can also print multiple payslips for employee/s using pretty much the same process, except you would select Payslips >> Multiple Pay Runs in the beginning of the process instead, and put in the date range you'd like payslips for.

To email payslips from the program, you will first need to have Lightning setup to email out by completing the steps listed here. Then, for the employees you'd like to have receiving their payslips and/or pay summaries via email, you will need to go to Employees >> Details >> Email Options, enter their email address, and tick Email Payslips? and/or Email Payment Summaries?. Once these two things are set up, you're free to email payslips out from the Pays tab using the same process as above, but selecting to Email payslips or Print and email payslips.

How Do I Create An Additional Pay?

To add a pay click on Create Pays, select the employee(s) whom you wish to record a pay for within that period. Then select the date you would like this pay to be processed or if it were a past pay, the date it was processed.

The tickbox at the bottom of the window which says Create Full Pay if ticked will filter the information from the Pay Settings for each employee.

If the additional pay is for a bonus or other irregular payment please see here for an example on paying a bonus, commision, etc.

If the additional pay is for a back payment please see here for an example of making a back payment.

If you need to delete an additional pay row from the pay run, please see here to learn how to do this.


How Do I Enter or Edit Past Pays?

To enter pays retrospectively in the program, you will need to go to the Pays tab, then hold down the Last Pay Run button on the left, and skip through to the pay period you'd like to start entering pays from. Once in the pay run you're after, you can edit pays like normal, then, once all relevant pays are complete, you can click Next Pay Run on the right and complete the next pay run, and so on, so forth.

If your employees' names are not in the pay run you skip back to, you can click on Create Pays to add them into the pay run. If you cannot add certain employees to a past pay run, please see the second paragraph of this FAQ.

It is also possible to edit past pays, though please bear in mind this would be done only in a few specific scenarios, as you do not generally want to edit any values that had been paid out at the time, being that you want to have accurate records of what was paid and accounted for at the time (even if there is a mistake in there).

If you find yourself in a scenario where you need to edit a past pay, you will need to skip back to the pay run in question, click Edit Pay to the right of the employee's pay you're editing, then click on the little padlock button at the bottom left of the screen to unlock the pay for editing, then proceed as usual.

How Do I Process a Pay?

To process a pay or pay run in Lightning Payroll, click on the Pays button at the top of the Lightning Payroll window.


When you click on the Pays button, you will be taken to the current or most recent pay run. If you want to go back to an earlier pay run, you can click Last Pay Run on the left. To go to future pay runs, click Next Pay Run on the right.


When processing a pay run, all pays are initially marked as Pending until they're either saved, or marked as complete.


To get started, you can click the Edit Pays button above the list of employees to edit the pays in order. Otherwise, you can click Edit Pay beside any employee's name on the right to edit that individual pay entry.


Once you have begun to edit a pay entry for an employee, you will be able to enter their hours worked for the pay period on the top left in the Hours section.


If you need to pay leave to an employee, you can add this in the Leave taken in this pay section. Click here to find out more on how to pay leave.


Tax and Super amounts are calculated automatically and are shown on the right.


Once you are happy with the employee's pay entry, click Save and Next on the bottom right to save and progress to the next employee or click Save and Close to go back to the pay run.


Once all the pay entries for your employees are marked as Complete, you will then be able to create the payslips and process Single Touch Payroll for this pay run.


Click here for more information on creating payslips, or click here for information on processing Single Touch Payroll.


You can also watch our video tutorial on how to process a standard pay in Lightning Payroll.

How Do I Delete A Pay?

To delete an Employee's pay, go to the Pays tab.

In line with the Employee you wish to remove, there will be a Complete button greyed out. You will find this to the far right of the program.

Right click on the Complete button and Delete.

If you cannot delete a pay, this is due to it having been sent through Single Touch Payroll. While you may not be able to delete a pay in this situation you can edit and resend if need be.

How Can I Reinstate A Terminated Employee?

If you would like to reinstate a terminated employee go to the Employees tab >> Click on Show Terminated Employees >> Select the employee you wish to reinstate >> Then click on Actions and Reinstate Employee.

How Do I Edit Existing Payslips?

If you need to make corrections to an employee's payslip, you will need to navigate to the relevant pay run for which that payslip was issued.

If the pay run was in the past, you can go back to earlier pay runs in the Pays menu by clicking the Last Pay Run button on the left. You can also click and hold the Last Pay Run button for 2 seconds and then release to see a list of previous pay runs for a quick selection.

Once in the appropriate pay run, you will need to click the Edit Pay button on the right hand side to make changes to the employee's pay. If the Edit Pay screen is locked, you can unlock it by clicking the padlock icon on the bottom left. Once you've made the necessary changes, click Save + Close.

You can generate a new Payslip that will show the changes made by clicking the Payslips button.

How Do I Enter A Public Holiday?

You can set up a pay rate for Public Holidays in the case that you would like public holidays separated from a full time employee's Ordinary Time; it is generally not advised to put through a full time employee's public holiday hours as annual leave, as full time workers will generally be paid for a public holiday as ordinary time.

To set a public holiday rate up for multiple full time employees, go to Company >> Pay Rate Groups >> +New Group and give the group of rates a name (eg. Public Holiday Rates). Next, click on the green plus symbol on the right and give the rate a description such as Public Holiday, leave all other settings as they are, and click Save. Finally, add all employees who will need this rate using the green plus symbol below the rate you have just created.

Now, when you go to pay a public holiday for a full time employee, you will select a second line of pay in Edit Pays and select your new pay rate, Public Holiday, and enter the amount of public holiday hours your employee did in this particular pay run.

How Can I Change My Pay Run Dates?

If your pay run dates need to change for pays going forward, simply go into Company >> Pay Dates and click Edit. This will let you select the Pay Period End Date of the appropriate pay schedule (weekly, fortnightly, monthly) and the pay runs will adjust dates accordingly.

Pay Period Start Dates cannot be edited and are a result of the previous pay period's end date.

If you have made mistakes with past, completed pay run dates then our support staff may be able to assist.

How Can I Adjust What is Shown on the Payslips?

If you would like to adjust what information is shown on payslips, you can do this for each employee in Employees > Pay Settings > Payslip Options.

This section allows you to select what types of information can be shown on payslips including:

  • Leave entitlements (including custom leave types)
  • Year-to-date totals for pay and super
  • Hours and rates of pay
  • whether leave balances are shown in hours or days.

Can I Process Pays In Advance?

If you would like to process pays in advance, you can do this by navigating to future pays using the 'Next Pay Run' button in the Pays screen.

From there, you can edit and save the pay entries as normal for each employee.

If the pays are being processed now but will not be paid until later, you will need to ensure that the processed date for the pays is set to the date the wages will be paid.

If you use the direct entry option to pay wages, please ensure the processing date for the direct entry is set to the date the wages will be paid to employees. Once the file is created, the processed date for each entry will be updated.

If you do not use direct entry files, you can edit the processed date for each entry manually by clicking the Edit Pay button on the right hand side and then clicking the pencil button on the top left of the employee's edit pay window. You will then be able to manually adjust the processing date. Repeat this until each entry for each employee has the correct processing date.

Can I Add My Company Logo to the Payslips?

You can add your company logo to the payslips by going to the Pays screen, clicking the Payslips button and selecting 'Configure Payslip Logo'.

Tick the box to turn Logos on and then select 'browse' to choose the image. You can adjust the height or width of the image by adjusting the measurements in the logo menu.

The preview will show you how the logo will look on the payslip. Once you are happy with how the logo will appear, click 'Close'.

How Do I Add a Missing Employee Into a Pay Run?

You can add employees into a pay run they're missing from in the Pays tab, by clicking on Create Pays from the particular pay run they're missing from, selecting the employee/s to add, then clicking Create. By having Create Full Pay? ticked at the bottom of the Create Pays screen, the program will use the hours and rate of pay set in Employees >> Pay Settings >> Pay Rates to pre-fill the pay for you; rest assured, you can still edit these pays like normal using the Edit Pays buttons on the main Pays tab.

If you have added a new employee and you're not able to find them on the Pays tab or add them using Create Pays, it is most likely that you have set an incorrect Start Date for the employee when adding them to the program. You can fix this by going to Employees >> Details >> Employment Dates and updating their Start Date to the correct date, then go back into Pays and the pay run you're after, and said employee should automatically now be in the list of people to pay.

How Do I Create Additional Pay Rates For Employees?

It's possible to set up various additional pay rates for employees in Lightning either individually or in groups.

To set up a pay rate to be applied to a single employee, go to Employees >> select the relevant employee from the list >> Pay Settings >> Special User Defined Pay Rates and add the rate in; this pay rate will then be available from the drop down list of pay rates in the Edit Pays screen.

To set up a pay rate that can be applied to a group of employees, go to Company >> Pay Rate Groups >> New Group and add in the pay rate, then Edit Employees to add said pay rate to a group of employees; this pay rate will then be available from the drop down list of pay rates in the Edit Pays screen for every employee you have selected.

What Kind of Reports are Available in Lightning Payroll?

Lightning Payroll offers a full suite of easy-to-use reports that can be accessed via the Reports menu in the program. You can change the font size and colour and export to pdf using the buttons at the top of any print preview screen.

Windows Smartscreen One

Ready to use reports include:

  • Pay reports
  • Taxation reports
  • Superannuation reports
  • Allowance and deduction reports
  • Leave taken and leave forecasting

You can also generate fully customisable reports through the Employee Report Builder and Pay Report Builder options in the Reports menu.

All reports allow you to view any current or historical data you have entered into Lightning Payroll.

All reports can be saved as .PDFs and printed. Select reports can also be exported from Lightning Payroll in .CSV format, allowing you to use them in Microsoft Excel.

How Can I Delete A Custom Report?

You can delete custom reports you've made in the past as they become obsolete to your business needs.

To delete a custom report, go to the Reports tab, then click on either Employee Report Builder or Pay Report Builder; wherever you created the custom report initially. Next, click on Open Report and select the report you'd like to delete from the drop down list, then click Load.  You will now see there is a Delete Report option at the top right of the screen, click this and then click Yes to delete the custom report.

How Do I Set Up Rostered Shifts in Lightning Payroll?

Lightning Payroll allows you to create shift types and schedule a roster for certain shifts and employees. These rostered shifts can then be used to fill-in your pays, saving time on data entry.

Please click here for related timeclock information.

Company Shifts

To begin setting up shifts in Lightning Payroll, go to Company >> Shifts.

To add a new shift type, use the green plus on the right. After that, just make sure to add any employees who may be required to work this shift at the bottom of this screen.

When editing a company-wide shift in the New Company Shift screen, the times, durations and pay rate are just defaults, or placeholders for this shift type. If a shift type is likely to change, that's fine, because any shift can be tailored for a particular employee or a particular date elsewhere, as described below.

Employee Shifts

If an employee tends to receive a particular pay rate, allowance or happens to work a shift on a regular basis you can configure this information under Employees >> Shifts.

All company shifts linked to an employee will be visible in this screen. To customise a shift for an employee use the pencil button to the right of the shift.

Note: If an employee has been assigned to any departments, these will be available for allocation at the bottom of this screen, and be reflected on departmental reporting once rostered shifts are imported into the Pays area, later on.

Roster Shifts

Rostered shifts can be viewed, edited and manually scheduled under the Rosters section of Lightning Payroll.

Repeating shifts will generate automatically when you first view a pay run within the Rosters screen. If you accidentally edit or delete any rostered shifts and wish to bring everything back to the starting point again, use the Reload Repeats button.

To add or edit rostered shifts to be worked during this pay run click the Edit Shifts button.

To add a new, one-off shift manually, use the green plus button. You will then see the New Rostered Shift screen. When creating a shift, keep in mind that break durations are not paid.


The Options button provides a way for you to customise the display of your Rosters screen. For example, you can set your business operating days and hours so that the program does not display unnecessary days or time periods on the screen. If you roster your pay runs two or three pay peridos in advance, you can set the default pay run offset, which tells the program how far into the future the Rosters screen should display by default.

Rostered Shifts and Pays

Rostered shifts are automatically used to populate the pay information in Lightning Payroll, whenever they have been created. The absence of a roster shift will mean pays generate using the employee's default settings configured under Employees >> Pay Settings.

You may wish to use the Rosters section, but not have rostered shifts modify your Pays. If this the case, go into Employee >> Pay Settings and tick the box to Ignore rostered shifts when generating pays.

My Company is Changing ABN and/or Ownership, What Do I Need to Do?

Below is some information on how to handle a change of ABN within Lightning Payroll.

Finalising For The Old ABN

Before changing details over to the new company, you'll want to ensure Single Touch Payroll and super payments have been sent off for the previous entity.

To finalise STP, just submit the final pay run to be paid from the previous ABN and when doing so, tick the box which says 'Final pay for the current financial year?'.

It is also recommended to finalise and pay any super owed from the old entity as normal now too, since sending super after updating the company details and ABN will result in the super coming from the wrong (new) entity.

Splitting & Restarting Financial Year YTD Amounts

If the company is changing ABN and/or ownership part way through a financial year, but all or most employees are remaining, you should split the financial year using the processed date of the final pay run to be made from the old company.


Company A's last pay is processed on November 10th (pay run start and end dates are not important)

Company B's first pay is to be processed one week later on November 17th.

You would split the financial year in Lightning Payroll to break on the 10th/11th.

Originally there would be one financial year (1/7 to 30/6).
After splitting, there would be two (from 1/7 to 10/11 and from 11/11 to 30/6).

To split the financial year and allow two distinct YTD amount boundaries (one for each of the two companies), go to Company > > Financial Years.

Click the pencil button to edit the current financial year and change the end date to match the final pay processed date of the old company and click 'Save'.

Then, click the green plus button to add a second copy of the financial year in question. Set the start date to be the day after the previous FY block (that you've just edited) ends.

Updating ABN And Other New Entity Details

Finally, update the Company > > Details section with the new company details and ABN.

Please also report the new ABN to our support team so that we can register it for SuperStream messaging with our gateway provider. You can do this yourself if you wish, by logging into your Lightning Payroll website account. Do not remove the old ABN if possible since you may need to do a follow up super payment at some point. Just add the new ABN under My Account >> Superstream Registration (Additional Companies).

Can I Merge or Split Companies Across Databases/Backups?

Business entities cannot be merged between backups/databases, however they can be split up. Splitting databases might be useful in cases where a solid chain of backing up has not been achieved between multiple user PCs.

To split entities into separate dbs/backups:

  • Make a backup with both companies
  • Delete company B
  • Create backup with remaining company A
  • Restore original (two company) backup
  • Delete Company A
  • Create backup with remaining company B

How Do I Add a New Employee or a New Company Entity?

Add a New Employee

Below are some links which you may find helpful when a new employee starts working for you.

New Employee Basic Information Sheet (PDF, Word Doc)

ATO Super Choice (Nomination) Form

ATO Tax File Declaration Form

Fair Work information Statement

To add a new employee, go into Lightning Payroll and click Employees >> Actions >> New Employee.

Add a New Company/Business Entity

Lightning Payroll does not limit the number of companies you can use in the software. To add a new company entity, simply click Entities >> Add new company.

How Do I Install Lightning Payroll on a New, or Replacement Computer?

Installing Lightning Payroll on a replacement or additional computer is a four step process:

1) Downloading the program: 
Download and install the program using the appropriate link below:

Download for Windows (Windows 7 and above)
Download for Mac OSX (Version 10.12 and above)

2) Installing the licence:

If you are given a free trial press Enter Paid Subscription Details to enter your details into our Licence Assistant (also found under Tools at the top of the screen) using your email address and six digit subscription ID number which can be found under Tools >> License Details in Lightning Payroll on the original computer.

3) Restoring your payroll data:
Firstly, create a backup of your current payroll data from Lightning Payroll on the existing computer (.lpb file) through Tools >> Create backup (or send one online through Tools >> Online Backups if you use that feature).

Then, in Lightning Payroll on the new computer, restore the backup (.lpb file) through Tools >> Restore backup (or restore the most recent backup sent online under Tools >> Online Backups if you use that feature).

4) Setting up Single Touch Payroll (STP):
To ensure you can continue sending STP submissions to the ATO on your new computer, you can export the machine credential from your existing computer. Please see our FAQ here for instructions.

Once these four steps are complete, you'll be ready to go.

One final note, while each LP subscription can be used on two computers at one time, this does not mean the data is automatically shared. Lightning Payroll is a desktop app and stores its data locally (on your PC hard drive).

If you run your program between two systems please ensure you keep both copies of the payroll data up-to-date by regularly creating and restoring backups. Our Online Backups feature is the best way to do this.

What Web Addresses and Domains Does Lightning Payroll Need To Communicate With?

Some users (such as many South Australian schools) require additional network configuration from their IT team to allow Lightning Payroll to properly function. The issue is mainly to do with network restrictions and blocked web addresses that Lightning Payroll needs to communicate with.

Below is a list of all web domains and urls that the program needs to access to function properly.

General Lightning Payroll URLs


How Do I Email Payslips or Payment Summaries from Lightning Payroll?

Lightning Payroll can email payslips and payment summaries to your employees, so long as you've configured the SMTP (outgoing email) server settings found under Company >> Email.

Lightning Payroll acts as a basic email client which can log in to your email account. Each email provider (such as Bigpond, Optus, Google, Yahoo, etc.) has their own SMTP server settings which may change from time to time. The Lightning Payroll support team cannot provide these email server settings. Usually the settings for your particular email provider are easy to find if you search the internet using terms like "(provider name) outgoing email settings", or "(provider name) smtp settings".

E.g. "Telstra Bigpond smtp settings", or "iiNet outgoing email settings".

You can also search for commonly used email settings under Company >> Email >> Search for Settings. This will use a third-party email settings provider to gather the server settings for you.

Once you have entered your SMTP settings under Company >> Email please click Send a test email to determine that you have entered the settings correctly.

If you cannot find working SMTP settings for your particular email account, it may be worth considering an alternative email provider.

Gmail Complexities

If you are opting for Gmail as your email provider within Lightning Payroll, please be aware that it can be quite tricky to setup. This is due to Google Mail offering a high level of security configurability and as a result, there are many hoops to jump through.

The best way to use Gmail for SMTP in Lightning Payroll is by going to and activating 2-Step Verification. Once you have activated 2-Step, you can then create a Google App Password specifically for Lightning Payroll (Other - Custom Name). For more information on managing App Passwords in your Google account, see - .

How Can I Add a New Employee?

Before you get started, it is recommonded you collect the following information from your new employee:

  • Tax File Number (TFN)
  • Bank account details (BSB, account name, account number)
  • Super fund details (fund USI and employee's member number)

Below are some links which you may find helpful when a new employee starts working for you:

To add a new employee, go into Lightning Payroll and click Employees >> Actions >> New Employee.

This will bring up the new employee assistant. Follow the prompts to fill out the employee's details. If you don't have all the available information now, you will still be able to add it to the employee's profile later.

NOTE: If the employee does not yet have a TFN, the ATO has more information about placeholder TFNs here.

You can also watch our short tutorial video on the company and employee setup process.

How Do I Get Started in Lightning Payroll?

If you are using Lightning Payroll for the very first time, there are a couple of steps you will need to follow to get up and running.

Step 1. Add your Company

The first step is to add your Company into Lightning Payroll. Lightning Payroll does not limit the number of companies you can use in the software. To add a new company, simply click Company >> Add new company on the top left of the Lightning Payroll window.

When adding a new company, you will need to enter your company name and ABN. You will also need to specify whether your pay period is weekly, fortnightly or monthly and specify which day of the week your pay period ends on.


Step 2. Add your Employees

The next step is to add your Employees into Lightning Payroll.

Before you get started, it is recommended you collect the following information from your employees:

  • Tax File Number (TFN)
  • Bank account details (BSB, account name, account number)
  • Super fund details (fund USI and employee's member number)

Below are some links which you may find helpful when a new employee starts working for you:

To add a new employee, go into Lightning Payroll and click Employees >> Actions >> New Employee.

This will bring up the new employee assistant. Follow the prompts to fill out the employee's details. If you don't have all the available information now, you will still be able to add it to the employee's profile later.

NOTE: If the employee does not yet have a TFN, the ATO has more information about placeholder TFNs here.

You can also watch our short tutorial video on the company and employee setup process.

How Do I Enter Existing Year-to-Date Figures?

If you are beginning part way through a financial year and need to add existing year-to-date (YTD) figures for your employees, there are three options to do this:

The first option is to enter all the previous pays for the financial year into Lightning Payroll. This can be done one-by-one in the Pays screen by navigating back with the 'Last Pay Run' button. This option is time consuming but it does provide the greatest amount of detail.

The second way is to generate a single pay for each employee immediately prior to the first official pay you will complete in Lightning Payroll and add in each employee's gross, tax and superannuation figures.

The third option is to complete a YTD adjustment for each employee in the Employees section. If you have the year-to-date (YTD) figures for each employee, you can enter these under Year to Date >> Adjust YTD Totals. Lightning payroll works forward from these amounts as you complete pays.

How Do I Connect Lightning Payroll to the Internet if I'm Behind an Authenticated Proxy?

If your company uses a network that involves an authenticated proxy you may have to enter settings under Settings >> Proxy to allow Lightning Payroll to access the internet. This means Lightning Payroll is able to keep you up-to-date with automatic update downloads and allows you to connect to the ATO via SBR and to the national Superstream network. All of these features require Lightning Payroll to have internet access. Contact your network administrator, or IT department for appropriate settings if you're unsure of what to enter.

Here's an example of a proxy setup:

How Do I Setup And Manage Different Users?

To further improve security, Lightning Payroll now allows you to create user profiles and set permissions for each user profile individually. This gives you complete control over who can access your Lightning Payroll and what data they can view or actions they can take.

Setting up users is very easy, but before you start, you need to set a password for the application administator. The application administrator can setup other users and determine what kind of access they have within Lightning Payroll.

Setting Up Users

To setup the application administrator, you'll need to go to Settings >> Password And Security and enter an application administrator password.

Once this is done, you can begin adding users to Lightning Payroll.

To do this, click on the Add New User button. You will be prompted to add a username and email address (for password reset emails), along with the user's login password. Finally, you can select which companies a user has access to.

Once you've clicked Save, the user will be added. You can then select the App Permissions assigned to that user for each section of the program.

App permissions fall into three categories:

  • Locked? (Cannot access section)
  • Read Only? (Can view, but not change data in section)
  • Editable? (Full access to section)

You can select which permission you'd like the user to have for a particular section by clicking in the appropriate box. The image below shows our test user John Doe being assigned 'Editable' permissions for the Employees and Pays sections of the program, but 'Read Only' permissions for the rest of the sections.

You may notice that the Settings, Entities and Tools sections have (G) next to them - these sections of the program are used across multiple companies (if you have multiple companies set up within Lightning Payroll). In the example above, if we had more than one company in Lightning Payroll, John Doe would have 'Read Only' permissions for Settings, Entities and Tools across all companies.

Editing or Removing Users

The application administrator can edit the permissions for users, or remove users whenever required.

Deleting a user will not remove any of the work they have completed in Lightning Payroll, it will simply prevent them from logging into the program going forward.

Logging In as a User and Logging Out

When opening Lightning Payroll, you will be asked to choose which user you would like to login as; select the user from the username drop-down menu, then enter the password for that user.

To log out of a user, simply close Lightning Payroll.

Forgotten Password

If the application administrator has forgotten their password, they can attempt to enter their password three times at the login screen; after the third failed attempt, a recovery password will be sent to the email address registered to the Lightning Payroll subscription.

The process is the same for a user who forgets their password, however, only the application administrator can change the user's password, by clicking Edit Selected User in the Settings >> Password And Security section of Lightning Payroll.

What is a Direct Entry User ID?

When creating a direct entry payment file, or processing super you may be prompted for a User ID, which usually resides under Company >> Bank Account >> User ID.

This is always a six digit number.

For most major banks (ANZ, Westpac, NAB) it is six zeroes (000000). For CBA it is 301500. For any other financial institution you will need to contact them and ask for the Direct entry User ID, or APCA ID.

Can I Import Data Directly into Lightning Payroll?

Lightning Payroll cannot import or export payroll data directly from - or to - another program or application.

If you are starting with Lightning Payroll after the current financial year has already begun, you can enter year-to-date (YTD) figures for each employee as YTD adjustments in the Employees section or by prefilling earlier completed pays in Lightning Payroll.

How Do I Enter Allowances?

Allowances for individual employees can be entered under Employees >> Allowances/Deductions >> Allowances using the green plus icon.

If you have common allowances to share amongst your employees, you can create company allowances under Company >> Allowances

If you wish to itemise an allowance separately within an end of year or Single Touch Payroll submission be sure to tick the Itemised? box when editing or creating your allowance.

If you wish to edit multiple pay allowances at the same time you can do so under Tools >> Retrospective Tool.


How Do I Setup Departments?

Departments can be configured in Lightning Payroll as a way for you to run reports on different cost centres within the application.

Departments are created under Company >> Departments.

Employees and their default pay % allocation can be assigned to departments under Employees >> Details >> Departments.

If a pay's departmental % allocation changes you can edit the department's allocation for specific pays under Pays >> Edit Pay/s >> Dept % (at the top of the window).

You can edit departmental % allocation for multiple pays/employees at once under Tools >> Retrospective Tool.

If you use shifts these too can be allocated to a department, under Employees >> Shifts, when editing a shift.

The best way to run reports for departmental pay data is via the Custom Reports area under Reports >> Pay Report Builder. Simple design your ideal report by selecting the appropriate columns and tick the box to Group by department.

How Do I Make Payments Using a Direct Entry Banking File?

The quickest and most accurate way to make bulk payments through Lightning Payroll is by using a Direct Entry (.ABA) file.

These files can be generated for pays and for super and then uploaded to most Australian banks, resulting in an automated, batch funds transfer. This means you can pay multiple employees at once or multiple super funds at once.

To create a direct entry file for Pays click Pays >> Direct Entry.

To create a direct entry file for Super click the Direct Entry button after sending Superstream messages within either:

  • Super Fund Deposits >> Superstream Contribution >> Superstream Summary
  • Super Fund Deposits >> Create Deposits >> Superstream Summary

Your bank should be able to guide you through the process of importing a direct entry file, but to help get you started we've rounded up some direct entry instructions for the most common banks. These instructions may change and are current as at March 2016. Please contact your financial institution for the most up-to-date instructions.

NAB Connect Instructions - (1300 888 413)
Westpac Instructions - (1300 655 505)
CBA CommBiz Instructions - (13 23 39)
ANZ Instructions - (13 33 50)

User IDs

When creating a payment file you may be prompted for a User ID, which belongs under Company >> Bank Account >> User ID. This is always a six digit number. For most major banks (ANZ, Westpac, NAB) it is six zeroes (000000). For CBA it is 301500. For any other financial institution you will need to contact them and ask for the Direct entry User ID, or APCA ID.

What Things Does Lightning Payroll Calculate?

Lightning Payroll is able to calculate your employees Super, Tax and Leave Accruals out of the box.

Lightning uses the latest tax tables built in to calculate the correct tax amounts for each of your employees. To make sure the correct tax is calculated for your employee, make sure you enter their correct Tax File Number in the Employees > Tax Rates > Tax Settings.

Lightning will also take care of calculating your employees' holiday, sick and long service leave entitlements on a pay by pay basis. You can choose which settings you'd like to use when setting up a new employee and Lightning will take care of the rest. You can also enter existing leave balances for employees.

Finally, Lightning is setup to calculate the standard 9.5% Super Guarantee by default. You can alter these settings in Employees > Super.



What Is Changing With Single Touch Payroll Phase 2?

In late 2021, Lightning Payroll will be updated to include Single Touch Payroll Phase 2 changes, required to be used by all employers as at January 1st, 2022.

These changes are mostly behind the scenes in Lightning Payroll, but you will notice a number of differences and you may also have to slightly alter the way you enter certain pay items. Key changes are described here, by the ATO, these are:

 See below for information on how each of these changes are handled in Lightning Payroll.

Disaggregation of Gross

Gross has always been disaggregated, or split-up to a degree when reporting to the ATO. Itemised allowances and ETP amounts have typically been broken apart. STP2 goes a lot further and splits out additional YTD amounts such as bonuses, leave, overtime and more. You will notice these in the new Single Touch Payroll reports (detailed and summary versions) now shown on the STP submission screen.

STP submission buttons

The Detailed Report shows individual employee YTD amounts grouped by income stream (described below), and totals broken down into disaggregated gross amounts. When comparing these amounts to other reports in Lightning Payroll (E.g. Pay Summary, Net Balancing, etc.) please keep in mind that anytime Gross amounts are mentioned, they are aggregated/combined, as disaggregation only occurs here, when submitting STP. Another point to note regarding non-STP/traditional reports is that gross values exclude sacrifices, raw gross values include sacrifices.

STP submission buttons

The Summary Report aims to provide an overview of the submission. It excludes detailed individual employee breakdowns and aims to show the disaggregation alongside total tax, RESC and deduction amounts.

STP submission buttons

Directors Fees

Directors Fees are now to be reported through STP. These are entered into Lightning Payroll via the Bonus/Commission sections, by ticking the Directors Fees? box.

Bonuses (including Directors Fees, Commissions, Return To Work Payments, etc.) are configured under Employees >> Allowances/Deductions >> Bonuses.

Directors Fees Employees

They can then be edited individually on pays via Pays >> Edit Pay >> Edit (beside Bonus/Commission).

Directors Fees Pays

Cents Are Included

Traditionally, when reporting to the ATO cents have been truncated/dropped. With this STP2 update you will notice that exact amounts are now being reported to the ATO, including cents. The End of Year section still truncates cents in the old way, so that payment summaries remain unchanged.

Back Payment Classification

Back payments must now be marked with a valid disaggregated gross category. This is a simple matter of choosing the right classification from the dropdown menu.

Back Payment Category

Employment and Taxation Conditions

In the past, Lightning Payroll would provide an option to include an employee's TFN declaration info (tax/employment settings) in the next new STP submission. STP Phase 2 now always includes this information by default, so there is nothing extra you need to do. It is most noticeably communicated via the new STP Tax Treatment code shown under Employees >> Tax Rates >> Tax Settings.

STP tax treatment code

Income Types (Aka. Income Streams)

Lightning Payroll has been approved by the ATO to handle the four following STP 2 income streams. These income streams are set as a side-effect of configuring an employee's general settings. An employee's income stream is visible under Employees >> Pay Settings >> Pay Rates

Employee income stream

  1. Salary and Wages
    • Most common, default income stream.
  2. Closely Held Payees
    • Set by ticking Employees > Pay Settings >> Pay Rates >> Closely Held Payee?
  3. Working Holiday Makers
    • Set by activating the Working Holiday tax scale under Employees >> Tax Rates >> Special Tax Rates.
  4. Voluntary Agreement
    • Set by ticking Manual variation of PAYG withholding/Voluntary Agreement (and including a valid ABN) under Employees >> Tax Rates >> Tax Settings.

When completing a pay it will use an employee's income stream at that time. You can view or edit the income stream of an individual pay via Pays >> Edit Pay >> Edit (beside Tax).

Pay income stream

Built-In Leave Types

When an employee is on leave you will now be able to select from a broad range of leave types. Each type is mapped directly to a specific STP 2 reporting category.

Leave Types

Removal of Pre-Tax Deductions

Pre-tax deductions are not able to be reported through STP2. We have found that most users were using these pay items to either:

  • reverse overpayments made to employees, or
  • handle salary sacrifices.

If you've used these pre-tax deductions throughout the financial year these will have been converted to negative backpayments automatically. This would suit the recouping of overpaid funds to an employee.

If you were using pre-tax deductions for salary sacrifices, it is recommended that you convert these items to a dedicated salary sacrifice pay item for the whole financial year which can be configured under Employees >> Pay Settings >> Salary/Wage Sacrifice and then controlled via Pays >> Edit Pay >> Sacrifice (on the right hand side). This will ensure that the amounts are correctly reported via STP2 as a salary sacrifice, since these are now reportable to the ATO.

Country Codes (Working Holiday Maker Change)

For Working Holiday Maker employees you will need to set their home country under Employees >> Tax Rates >> Special Tax Rates. Lightning Payroll will request this when sending STP 2 for the first time.

Child Support Deductions

Lightning Payroll has included classification of STP 2 child support deductions (garnishee and standard deduction types) for several months now, editable under Employees >> Allowances/Deductions >> Deductions. These classifications and amounts are now able to be reported to the ATO via STP2. If you do not wish to report child support deductions or garnishee amounts, just set the deduction classification to Normal under Employees >> Allowances/Deductions >> Deductions. If you need to change deduction classifications on past pays we recommend you use our Retrospective Tool under the Tools menu at the top of the screen.

Child Support Deductions

Reporting Previous Business Management Software IDs and Payroll IDs

Occassionally - though very rarely - it may be necessary to report changes in employee IDs and company BMS IDs. This might occur when you've changed your business structure or changed software and can't zero out or finalise previous records. You can now view and edit (not recommended) these employee and BMS IDs under Employees >> Details and Company >> Details, respectively.

Time In Lieu

When recording a time in lieu custom leave item you will now need to mark it as such under Company >> Leave Balances so that it can be reported correctly through STP2. Time off in lieu (TOIL) is considered overtime when cashed out, and will be reported as such in STP 2.

Time In Lieu

Termination Reasons

When terminating an employee you will now notice a new dropdown box where you can specify the detailed reason why an employee is being terminated. This helps the ATO and Services Australia from requiring an employment separation certificate.

Termination Reasons

The ATO Said I Need To Get My Machine Credential From My Payroll Provider - Is That Right?

Lightning Payroll requires users to obtain an ATO machine credential keystore file so that they can send Single Touch Payroll from the software to the ATO each pay run.

We often get calls from users requesting assistance with ATO machine credential keystore files. These files are generated and managed on the ATO's Relationship Authorisation Manager website and are 100% out of the control of our support staff here at Lightning Payroll. We are unable to support the ATO's websites and/or software.

You can instead contact the ATO's Technical Helpdesk on 1300 139 373 between 7.00am and midnight, Monday to Friday.

It is sadly a very common occurrence that some ATO staff do not seem to have enough training to understand what users are asking for when requesting assistance with machine credentials. If you speak with their helpdesk and are told that machine credentials come from your payroll provider this is false. We recommend you request to speak with an ATO helpdesk Team Leader so that they can be made aware that their staff are mistaken.

Sometimes they might also tell you that you must provide Lightning Payroll's ABN or software ID to register - this too is incorrect. You just need a machine credential. Lightning Payroll is desktop based, not web-based; only web-based software require ID and ABN registration.

As you can see here in the ATO's machine credential documentation, the machine credentials come from the ATO, not from payroll providers such as Lightning Payroll. There is nothing you have to do in Lightning Payroll to register or connect a machine credential to the ATO; you simply obtain the file from their RAM website (using their ATOBE software extension) and Lightning Payroll knows where to find it.

We have raised this issue with the ATO a number of times - hopefully they will improve their training in future.

Machine Credential Tips and Useful links

What is Single Touch Payroll?

Single Touch Payroll (STP) is a new initiative for reporting your employees' tax and super information to the ATO. It is required for all businesses to begin using STP from the 1st of July, 2019.

STP is built into the latest version of Lightning Payroll and only requires a valid ATO Machine Credential installed on your computer to use.

STP allows you to report the rolling year-to-date (YTD) figures for each employee at the end of every pay period. It doesn't change how you pay your employees or how you make their superannuation contributions. STP is a reporting tool only.

For more information, you can visit the ATO's STP page here.

What is the Difference Between a New Event and an Update Event?

There are two types of STP messages you can send from Lightning Payroll, a New Event and an Update Event.

A New Event is the most common submission type and is the recommended way to send Single Touch information to the ATO. It basically means you are submitting new pay information.

Update Events are most commonly used to submit amendments made to pay runs already lodged. They can also be used for submitting YTD figures for terminated staff who are not available for a New Event submission due to not being paid within the pay period being lodged.

New Events should not be regularly sent for pay runs processed/paid in the past. The ATO will allow past processed dates on new/pay events, but they discourage it.

If you send a new/pay event for a past pay date you will see this warning


Update Events cannot be sent for pays processed/paid in the future.

Lightning Payroll collects YTD values using the pay processed/paid date, and lodges using the pay period's most recent processed date within the same financial year.

For more information on STP events and guidelines, see here.

Why Aren't STP Totals Showing in the ATO Online Services Page?

All references below are taken from the ATO Single Touch Payroll Business Implementation Guide v3 (published May 2018). This is the official document used to implement business logic regarding Single Touch Payroll.

Within the ATO's Online Services For Business page (under Employees >> STP Reporting) you can see a record of your STP event history, which will coincide with the more detailed records shown in Lightning Payroll under Pays >> Single Touch >> Single Touch Mailbox. In the Online Services For Business page you will see totals for STP Pay Events, but not for Update Events.

The W1 (gross salary and/or wages) and W2 (PAYG tax withholding) STP pay run totals can cause a lot of confusion, as do the two event types (Pay Event and Update Event). In Lightning Payroll we often refer to Pay Events as New Events.

The main difference shown in the Online Services For Business page is that Pay/New Events contain W1 and W2 totals, where Update Events do not. This is not a Lightning Payroll rule, this is an ATO STP rule shown in the B.I.G. document linked above, and explained below.

Said another way, the reason your pay run totals are not showing up in the Online Services For Business page is because you are sending Update Events, when you should be sending New/Pay Events. This is not a major problem however as the main point of STP is to report employee YTD amounts and these will be reported in full either way. The pay run totals shown in the Online Services For Business page are just used for prefilling BAS amounts, as mentioned below.

If you are unable to select employees to send in a New Event it is because you are sending STP for pays with processed dates too far in the past. 14 days is as far back as fixups are allowed, and past dates are discouraged by the ATO.

You must send a New Event on or before pay day for pay run W1 and W2 totals to be included in the message and on the Online Services For Business page.

If your processed dates are incorrect you will need to fix these in Lightning Payroll under Pays >> Edit Pay using the pencil at the top of each Edit Pay screen. If you use direct entry to pay your staff, your pay processed dates will be automatically adjusted to reflect the processing date of your direct entry (ABA) banking file.

Pay Event (New Event)

A Pay Event (New Event in LP) is the primary STP message type. "Whenever an employer makes a payment to an employee that is subject to withholding they are required to lodge a Pay Event message with the ATO on or before the date the payment is made." B.I.G. page 17.

Update Event

The Update Event allows the employer to report changes to employee YTD amounts previously reported, or to report fix-ups within 14 days of payment. The update event cannot be used to supply (B.I.G. page 19):

  • Employer ‘Total gross payments’ and ‘Total PAYGW Amounts’.
  • The onboarding section (which contains the employee withholding details and declaration).

"As there is no associated payment to the employee when changes are reported via the update event, the employer pay period totals for gross payments and PAYG withholding cannot be included in an update event."

What Are The Pay Event W1 and W2 Totals Shown in the Online Services For Business Used For?

"For an employer who pays their PAYG withholding with their BAS, the ATO will aggregate W1 and W2 across all BMS IDs for pre-filling of the employers BAS." B.I.G. Section 3.1.2 (part 3).

How Do I Correct These Totals?

These totals cannot be corrected, but since they are used only for BAS prefilling, you can edit the prefilled amounts as needed when paying PAYG with your BAS.

Where Can I Find More Information?

To read more about the rules of STP, please visit the ATO web site.

How Do I Setup JobKeeper Payments in Lightning Payroll?

The JobKeeper payment is intended to provide wage subsidies to businesses that are significantly affected by COVID-19. It is to be administered by the ATO.

18/09/2020 Edit: JobKeeper has been extended until 28/3/2021, please see here for more information on how JobKeeper extension features work in Lightning Payroll.

For answers to most payroll related Coronavirus questions please see the Fair Work website here.

If you are confident that your business and employees are eligible to receive the Australian Government's JobKeeper payments, these are to be best entered into Lightning Payroll as an allowance.

For more detailed information, please see the ATO JobKeeper (Employers) page as it contains the best information regarding paying JobKeeper and the full application process.

The full ATO enrolment process is available here. Step 2 on this enrolment page (Identify and maintain your eligible employees) can be handled by Lightning Payroll as we are both STP and JobKeeper enabled. How to do this is described below.

JobKeeper Payment enrolment is open to eligible employers until the program closes. Your clients must enrol and identify their eligible employees by the end of the month they wish to claim for. A monthly business declaration will then need to be completed from the 1st to the 14th day of the following month.

For detailed information on accruing and taking leave when receiving JobKeeper payments please see the Fair Work Australia website.

There are two parts to recording JobKeeper payments in Lightning Payroll:

  • Step 1 of 2: Making a JOBKEEPER-TOPUP allowance
    • This step is only required for employees earning under the minimum amounts, thus requiring a topup of their earnings
  • Step 2 of 2: Reporting JobKeeper through STP
    • Required for all JobKeeper-claimed employees

Note: For JobKeeper features you will need to be on the latest version of Lightning Payroll. Click Check for updates now? at the bottom of the program to speed up the update process.

JobKeeper in LP (Step 1 of 2): Making a JOBKEEPER-TOPUP Allowance

If you have employees earning under the JobKeeper minimum amount and wish to claim for them, a topup payment will be required to maintain eligibility. This JOBKEEPER-TOPUP allowance is only needed for such situations. JobKeeper (Step 2 of 2) mentioned below, is required for ALL employees you wish to claim JobKeeper for.

Regarding Backpayment of the JOBKEEPER-TOPUP for April, the ATO says:

"For the first two fortnights (30 March – 12 April, 13 April – 26 April), we will accept the minimum $1,500 payment for each fortnight has been paid by you even if it has been paid late, provided it is paid by you by 8 May. This means that you can make two fortnightly payments of at least $1,500 per fortnight by 8 May, or a combined payment of at least $3,000."

Lightning Payroll lets you add the backpayment in either the current pay as a lump sum, or separately within each individual pay within April (by clicking Last Pay Run and editing each pay). Both methods look the same within STP as it only sends an employee's YTD totals. Do not use the Backpayment box however. JOBKEEPER-TOPUPs must be recorded as allowances, just like we describe below.

Below is an example of how a typical weekly JOBKEEPER-TOPUP allowance would be configured. An allowance can be created under one of two places:

  • Company >> Allowances
    • Use a company allowance if you wish to apply the JOBKEEPER-TOPUP allowance to multiple employees at the same $ amount per pay.
  • Employees >> Allowances/Deductions >> Allowances
    • Use employee allowances if you want to set each employee's topup $ amount differently between staff (e.g. One person earning $400 weekly requires a $350 topup to reach the minimum $750. Another person earning $700 weekly would need a $50 weekly topup).

For employees whose pay and topup amounts change from pay to pay, either allowance type would suit as you will still need to manually calculate and edit the topup amount, dependant on each pay in Pays >> Edit Pay/s.

Once you are in the appropriate allowance section click on the green plus button to add a new allowance.

  • Enter the Description as JOBKEEPER-TOPUP (typed exactly like that).
  • Set the Amount as required:
    • Minimum gross pay amounts are $1500 fortnightly, $750 weekly or $3000 monthly (with the exception of $4500 for the month of August since it has three fortnights). Monthly payers can also opt to pay $3250 consistently if they prefer. The example image below is set to $0 by default, which suits constantly varying pays. Just top up the allowance from $0 to the required amount on each pay as you go.
    • Only pay full amounts if the employee has been stood down.
    • For employees earning under the JobKeeper amount, pay them as usual and 'topup' the difference using this allowance, via the usual Edit Pays screen. The ATO site above says "If your eligible employees earn less than $1,500 per fortnight before tax, you must pay them at least $1,500 for each fortnight to claim the JobKeeper payment. This is a ‘top up’ of their salary or wages and will ensure they remain eligible."
    • For employees earning over the JobKeeper amount, simply pay them their usual pay. There is no need to use this allowance.
  • Set 'Classification' to 'Other'
  • Enable 'Taxable?'
  • Enable 'Itemised?' to separate the allowance out in the STP report
  • Disable 'Included in Super Calculations?' as super is not required on JobKeeper amounts.

If you're creating a Company Allowance don't forget to add eligible employees to the new allowance underneath, using the green plus.

You can now edit their pay under Pays >> Edit Pay/s using the JobKeeper allowance. Simply enter ordinary time and other pay items like normal, then edit the JOBKEEPER-TOPUP allowance to make up the difference so that the gross matches the required minimum mentioned above.

JobKeeper in LP (Step 2 of 2): Reporting JobKeeper through STP

Once you have completed your JobKeeper eligible pays you need to mark intended employees as eligible to report JobKeeper through Single Touch Payroll. To do this go into Employees >> Tax Rates >> JobKeeper Settings and tick the box to mark the employee as eligible.

Eligibility dates are preconfigured to apply the entire 13 week ATO JobKeeper period, but you can reduce this date range if you only want to apply for a shorter JobKeeper period for this employee.

This will mark pays between these dates as claimed for JobKeeper and report appropriately through Single Touch Payroll. You will be able to see the special ATO JobKeeper claim reference codes showing up in your STP report and lodgements.

These FN (Fortnight) reporting codes are automatically handled by Lightning Payroll using the eligibility dates you have set under Employees >> Tax Rates.

The JOBKEEPER-START-FN code represents the fortnight they started JobKeeper, and the JOBKEEPER-FINISH-FN code represents the first full fortnight they become ineligible for JobKeeper. These codes should not change with each pay period.

Why is The ATO's Website Not Showing a List of JobKeeper Eligible Employees?

From a recent ATO software developers newsletter:

"A business that has reported JobKeeper codes in their STP software will only see the number of eligible employees that have been reported, not a list of each employee.... They will need to check the number is correct or edit the number."

You Do Not Need To Change Your Pay Cycle

The JobKeeper scheme relies on processed date (date the payment was made to employees), not the pay run dates. Please see the fortnight codes tables below for an example.

From the ATO:

"Regardless of the frequency of regular pay cycles or out of cycle pay periods, or the pay period start and end dates, the $1,500 per fortnight applies to the paydays (payment date) within the defined fortnights and from which fixed fortnight the payment applies. Special rules apply for payments within the month of April and for employees receiving monthly pay."

How Do I Create a Machine Credential?

Machine credentials are what allow your payroll data to be securely sent and verified by the ATO when using Single Touch Payroll. The following FAQ will guide you through the steps to download a machine credential for your business. There is nothing you need to do in Lightning Payroll to link your machine credential, it is automatic so long as you complete the steps below.

If you get stuck, please contact the ATO's Technical Helpdesk on 1300 139 373 between 7.00am and midnight, Monday to Friday. If the ATO representative advises that you need to get an SSID, ABN or Software ID from us, this is not correct. You simply need a Machine Credential. Please see here if you are told this.

Also, we have been informed that if your business is a trust you will likely need to contact the ATO hotline above to have them manually link you to your ABN, or else it will not be available in RAM.

Note: This guide requires you to use Google Chrome web browser. If you don't have Google Chrome installed on your computer, you can visit the Google Chrome page here to download it.

What Do I Need To Do?

A) Install Both Required Software

  1. Download the myGovID app to your smart device and set up your myGovID using your identity documents.
    • Available on the App Store for Apple, or on Google Play for Android.
  2. On your Lightning Payroll computer, open Google Chrome and click the link here to visit the Chrome Webstore page. You will need to add the ATOBE extension to Chrome before continuing.

B) Create and Download Your Machine Credential

Once you have installed the required software, you can create your machine credential. These new credential files last for two years, so this process might seem painful, but it is not going to be a frequent exercise. For detailed instructions on creating a machine credential (including pictures), see here.

The usual process is to:

  1. Open your myGovID app on your smart device, then login to RAM using the same Chrome or Firefox web browser that the ATOBE extension was installed onto.
  2. Click View or manage authorisations, machine credentials and cloud software notification.
  3. Click on your business/company name (not on 'View').
    • If the business is not visible you need to click Link your business on the main RAM entry page, then follow the prompts. Only the ABN's principal authority can claim the ABN. Update your ABN details with the Australian Business Register if your ABN is not linkable in the RAM website.
    • If the business is visible, but unclickable, then you do not have correct administrative privileges and will need to contact your principle authority or the ATO for assistance.
  4. Click Manage Credentials at the top of the page.
    • If this option is not visible you are not a machine credential administrator and need to contact your principle authority or the ATO for assistance.
  5. Click Create Machine Credential and follow the prompts. Please take note of the following tips:
    • If you get a Software Required error, the browser extension software is not being detected. We have an FAQ on this.
    • When creating your machine credential, do not change the keystore path as Lightning uses this to automatically detect the new keystore file.
    • Create and remember a new keystore password as this will be required to submit through Lightning Payroll. This password cannot be reset.
    • The credential name is up to you and usually is a word which represents the PC you use Lightning Payroll on (E.g. Reception, admin, office, etc.). It cannot contain spaces or special characters.
    • Agree to the terms and click Download at the bottom of the page.
    • Lightning Payroll will then automatically detect your new keystore. You will be able to select it and enter the new password (the previously saved password will need to be overwritten) when you next submit STP through the program.
  6. Repeat steps 1-5 for any additional ABNs you process STP for on this computer.

C) Test Your New Credential

To test your new credential has been installed correctly, go into the Pays screen within Lightning Payroll and click Single Touch >> Submit Payroll to the ATO. On the preview/submission screen (seen after you click Next) you should see the new credential in the dropdown with a new expiry date of at least 2022. 

If you have followed all of the step above but you can still only see the expired AUSkey credential, you might be running an old version of Lightning Payroll. Please see our FAQ here for help updating.

Why Can’t I Select Employees For Single Touch Payroll?

When submitting Single Touch Payroll around July 1st you may discover that no employees are available for selection. This can be due to a couple of different reasons. Please check for updates (at the bottom of Lightning Payroll) and ensure you are on the very latest version before continuing.

The most common reason is the selected event type (new event vs update event). New/pay events can only include unsubmitted employees who were paid within the chosen pay period, whereas update events are broader and can include anyone paid within the financial year, including terminated staff.

Empty STP Employees

If no employees are available for either new or update events, there is likely a conflict with the pay run processed date and the financial year boundary dates. Please ensure that the most recent processed date of the pay run falls within the desired financial year dates under the Company >> Financial Years tab. You can then either edit the pay processed dates or the financial year boundaries to correct the issue, depending on which is most appropriate for your situation.

Why Am I Having Problems When Trying to Submit Single Touch Payroll?

Below are the most common Single Touch sending errors you might receive:

Failed to collect Authentication Token:

If you are receiving this error, you will need to check the following:

  • Check the credential dropdown, for any other credentials for the same ABN.
  • Make sure your computer's time, date and timezone are exactly correct, to the minute.
  • Check that you are connected to the internet. Security software may be preventing Lightning Payroll from accessing your computer's internet connection. To test LP's internet connection go into Tools >> Licence Assistant and you should see an Online Licence Install window. If you do, LP is connected and you may close the Licence Assistant. If instead you see a Local Licence Install window then you will need to configure, update and potentially disable your security software and try again as it is preventing LP from connecting to the internet.
  • Check that there are no errors displayed on the ATO machine credential server page.
  • Ensure your Machine Credential is not revoked or expired (when you select it from the Credential drop down under 'Submit Single Touch', it should say VALID on the right hand side, and have a decent expiry date). Even if it does say valid it may still be revoked on the ATO's servers. If your credential has expired, you will need to renew it. If it has been revoked you will need to make a new credential.
  • If you are are sending with proxy enabled under Settings >> Proxy try sending STP without proxy being enabled. Many users no longer need proxy enabled if it is preventing STP from sending.
  • If your error log says 'LookupError: unknown encoding: idna' your program is not installed correctly. Please reboot your pc and reinstall using the free trial links at our homepage.

Once you have checked all the above, please try resubmitting. If you still receive the same error, please login to the ATO Relationship Authorisation Manager and contact our support team so they can help you investigate the status of your credential.

Lightning Payroll freezes after clicking 'Submit to the ATO' (Windows users):

If this issue is occuring, please do the following:

  • Close Lightning Payroll.
  • Right click on the Lightning Payroll desktop shortcut and select Properties.
  • Click on the Compatibility tab.
  • Make sure run in compatibility mode is unticked.
  • Click Apply and then OK.
  • Reopen Lightning Payroll and try submitting again.

How Do I Fix Errors Regarding JobMaker Hiring Credit In Lightning Payroll?

Note: Please click here to see how to setup JobMaker in Lightning Payroll as this FAQ assumes you are already using the scheme and related features in the software.

The ATO have released a general JobMaker Troubleshooting Guide which you can access here.

The advice below is taken from the ATO's Technical Document for JobMaker and Single Touch Payroll.

How Do I Cancel A Mistaken JobMaker Nomination?

If you have accidently enabled JobMaker for an employee, go into Employees >> Tax Rates >> JobKeeper/JobMaker Settings and press the green plus button in the Active JobMaker STP Flags table. You will then be able to add a nomination cancellation flag code as seen in this image.

Resending STP will pass this cancellation code to the ATO. Once sent, you will then be able to disable JobMaker for the employee in their JobKeeper/JobMaker settings area.

JobMaker Nomination Cancellation

How Do I Cancel A Period/Quarter This Employee Should Not Have Been Reported As Eligible For?

If you have accidently sent a JobMaker period code for an employee in which they did not actually work an average of 20 hours you will need to add a matching cancellation flag code for that employee and report it through STP.
To do this, go into Employees >> Tax Rates >> JobKeeper/JobMaker Settings and press the green plus button in the Active JobMaker STP Flags table. You will then be able to add a manual period cancellation flag. This image demonstrates how a cancellation flag would be created against JobMaker period 1, required in the case where period 1 was declared for this employee via STP and they hadn't actually worked enough hours, for example. 

JobMaker Period Cancellation

Why Am I Receiving a Software Required Error in the Relationship Authorisation Manager (RAM) site?

If you're attempting to create a machine credential in the Relationship Authorisation Manager (RAM) but are receiving the following 'Software Required' message, you will need to ensure you have installed and enabled their ATOBE browser extension software.

Please see the ATO's support page for instructions on how to solve this issue.

If you get stuck, please contact the ATO's RAM helpline on 1300 287 539 (select option 3 for RAM enquiries) between 8.00am and 6.00pm, Monday to Friday.

How Do I Setup JobMaker In Lightning Payroll?

From the ATO:

"On 6 October 2020, as part of the 2020–21 Budget, the government announced a new incentive for businesses to employ additional young job seekers called the JobMaker Hiring Credit. The JobMaker Hiring Credit is administered by the ATO.

Eligible employers can access the JobMaker Hiring Credit scheme for eligible additional employees they hire between 7 October 2020 and 6 October 2021, for a maximum claim period of 12 months from their employment commencement date.

Through the JobMaker Hiring Credit scheme, eligible employers may receive payments of up to:

- $200 per week for each eligible additional employee aged 16–29 years old inclusive.

- $100 per week for each eligible additional employee aged 30–35 years old inclusive."

Click here to download the ATO's JobMaker employee eligibility fact sheet.

How Do I Claim JobMaker?

  • Register your business with the ATO before enabling your employees in Lightning Payroll. Part of checking business eligibility requires an active employee headcount as at 30/9/2020. You can use our Active Employees Headcount report for this, found in the main Reports screen of Lightning Payroll.
  • Enable your eligible employees, shown below.
  • Use Single Touch Payroll (via Lightning Payroll), and your JobMaker-enabled employees will be nominated for the JobMaker Hiring Credit with the ATO.

Which Employees Are Eligible?

Employees are eligible if they:

  • are an employee of the entity during the JobMaker period
  • are aged 16 to 35 years old when they started employment
  • started employment on or after 7 October 2020 and before 7 October 2021
  • worked or have been paid for an average of at least 20 hours per week they were employed in the JobMaker period
  • have given a JobMaker Hiring Credit employee notice to the employer
  • have not already provided a JobMaker Hiring Credit employee notice to another current employer
  • received the Parenting Payment, Youth Allowance (other than on the basis that the individual was undertaking full-time study or was a new apprentice) or JobSeeker Payment for at least 28 consecutive days (or 2 fortnights) in the 84 days (or 6 fortnights) prior to starting employment.

How Do I Enable JobMaker For An Employee In Lightning Payroll?

JobMaker (like JobKeeper) is enabled under Employees >> Tax Rates >> JobKeeper/JobMaker Settings. Simply select the option which says Tick this box to claim JobMaker Hiring Credit for this employee via STP.

JobMaker Settings

Lightning Payroll will automatically generate special STP flag codes as required by the ATO using a combination of factors:

  • Employee's start date
  • Employee's date of birth
  • Employee's hours worked

Start date and date of birth are used to detect an employee's eligibility. If they do not meet basic criteria Lightning Payroll will prevent you from enabling JobMaker for that employee.

The box at the bottom of the above image (Allow Lightning Payroll to assist with JobMaker average hours checking and flag codes?) should usually be left alone as it allows the program to check whether an employee has met the 20 hours average hours worked for each JobMaker quarter.

Please double check the claim period codes are appearing (shown in the STP submission report) at the end of each JobMaker quarter to ensure your claimed employees have met the minimum hours test or else they will not be nominated through STP for that quarter.

Lightning Payroll will also remind you about JobMaker with new employees and rehires if they meet basic date criteria.

JobMaker Prompt

What If The Employee's Recorded Average Hours are Not Eligible, But They Actually Did Work An Average 20 Hours?

You can manually enter period flags if you wish to manually declare an employee's minimum hours were met for any JobMaker quarter using the Active JobMaker STP Flags table. Click the green plus to manually insert a JobMaker Hiring Credit Eligibility Period, and choose the quarter in which the employee met the minimum work hours test (20 hours weekly).

Note: If you enter a manual flag it will not interfere with Lightning's automatic flag checking, causing duplicates. Lightning Payroll will not add a flag code which already exists.

JobMaker Manual Flag

Source: ATO's Guidance Document for JobMaker and Single Touch Payroll.

What Is Changing With The JobKeeper Extension?

The ATO have released rules and information relating to the JobKeeper extension. Please see their page on the topic here, or click here for the technical STP extension document.

The main difference going forward into the JobKeeper extension periods (post 27/9/2020) is that the payments are now tiered depending on an employee's past workload.

What If My Employees Aren't Eligible for the JobKeeper Extension?

If you have been claiming JobKeeper and wish to stop claiming for any or all of your employees you just need to adjust their JobKeeper eligibility end date/s. This can be done under Employees >> Tax Rates >> JobKeeper Settings.

Do not untick the main JobKeeper eligibility tickbox. Simply change their JobKeeper eligibility end date to the paid/processed date of the last JobKeeper-related pay you will be making to each employee. If claiming until the end of the scheme, do not change this date, as the automatic, default end date is ideal.

E.g. Ending JK on 27/9/2020 will generate A JOBKEEPER-FINISH-FN14 code for an employee, which tells the ATO that they are ineligible for JobKeeper starting JK fortnight number 14.

How Much Do I Need To Pay Employees In Each Of The Two Extension Periods?

Tier 1 employees are eligible employees who worked for 80 hours or more in the four weeks of pay periods before either 1/3/2020 or 1/7/2020.

Tier 2 employees are all other JobKeeper eligible employees. 

The extension periods and updated amounts are as follows:

  • Extension 1: from 28/9/2020 to 3/1/2021
    • Tier 1: $1,200 per fortnight (before tax)
    • Tier 2: $750 per fortnight (before tax).
  • Extension 2: from 4/1/2021 to 28/3/2021
    • Tier 1: $1,000 per fortnight (before tax)
    • Tier 2: $650 per fortnight (before tax).

See the ATO's website for information on reporting business participants, as Lightning Payroll only reports JobKeeper via STP for employees.

You don't need to remember tier levels or JK amounts during each period. For convenience, Lightning Payroll will display the appropriate amount at the top of each employee's Edit Pay window.

Note: If you cannot see this blue text message at the top of the window it means the employee is not JobKeeper enabled (under Employees >> Tax Rates >> JobKeeper Settings), or that the current pay's processed date is outside of the JobKeeper extension period (28/9/2020 - 28/3/2021). Press the small pencil button at the top of the Edit Pay window to change the processed/paid date.

In this example, it is for a Tier 1 employee, paid weekly, during JK extension period 1.

JK Extension Pays Label

Note for MONTHLY pays: The prompted amount shown in your monthly employee's Edit Pay window is calculated using the average JK monthly amount method by default. You can change this setting to calculate based on the number of fortnights ended within the month under Settings >> Time/Display Settings by unticking the box which says Use average-out method for calculating monthly JobKeeper amounts.

JK Extension Monthly Average Setting

What Do I Need To Do In Lightning Payroll?

Lightning Payroll does its best to automatically detect each employee's tier, so you will not likely need to change any employee settings if you are already claiming JobKeeper.

Please review your employees' tier levels to ensure they are accurate.

Note: There are still some reasons why Lightning Payroll's automatic tier assessment may need manual setting up, for example:

  • Difference of interpretation of the ATO's criteria. Since pay cycles can vary quite a bit, Lightning Payroll calculates an employee's average hours starting at their most recent pay date within the months prior to 1/3/2020 or 1/7/2020, then calculates the four weeks before and inclusive of this date (27 + 1 days). This is more complicated than just averaging hours worked in February and June. Exceptions to an employee's Tier 1 eligibility could include when:
    • they have taken unpaid personal leave during the pre-March or pre-July reference period and this is not representative of their typical hours.
    • their first pay cycle ends on or after 1 March or 1 July.
    • employed part-way through the reference period.
  • Lightning Payroll can only detect hours it is aware of. If you pay your employees using non-hourly pay rates you will need to manually set tiers.

To check or change the automatically determined employee tier levels go to Employees >> Tax Rates >> JobKeeper Settings >> Should this employee be classed as Tier 1 for the JobKeeper extension?

JK Extension Tick

The program will also add an employee note with basic reasoning why that tier level was auto-marked.

JK Extension Tiers Note

You will need to ensure you correct the amounts paid each pay period (the program will prompt the appropriate amount; see above image). These JobKeeper reductions might require you to make some JOBKEEPER-TOPUP allowance amount changes. Allowance templates are configured under either:

  • Company >> Allowances
  • Employees >> Allowances/Deductions >> Allowances

Either allowance template type allows you to edit an individual allowance amount within an individual pay. These individual pay allowances are edited under Pays >> Edit Pays >> Allowances/Deductions >> Allowances.

Why Does The ATO Think I Have More JobKeeper Employees Than I Actually Do?

The most likely cause of this issue is usually terminated employees who were originally receiving JobKeeper.

This is a common issue and is due to a quirk in the way the ATO setup reporting the 'end' of claiming JobKeeper for an employee.

When an employee is terminated, or otherwise is no longer eligible for claiming Jobkeeper, a finish flag with the appropriate fortnight number is required to be sent off to the ATO indicating the first new fortnight in which that employee will NOT be receiving JobKeeper anymore.

The issue that arises is that the ATO do not allow payroll programs to report this finish flag until the next JobKeeper fortnight is reached. When an employee is terminated, you typically don't continue including them in single touch submissions because they have no new data to report. This means that the finish flag for the terminated employee remains unreported.

The easiest way to solve this is to firstly check that the JobKeeper eligibility end date is for the employee is set to when they finished employment. This can be checked in Employees > Tax Rates > JobKeeper Settings (make sure to tick 'show terminated employees' first).

Once the correct end date is set, all you'll need to do is send off an 'Update' event in single touch and select the employee in question when sending it off to the ATO.

Alternatively, if the employee was terminated in the previous financial year, navigate back to your last pay run of the 19/20 FY in June in the Pays menu and, in the last pay run in June, send off a final STP message once more for this terminated employee.

A finish flag beginning with JOBKEEPER-FINISH-FN should be reported on the bottom left of the employee's single touch preview.

Resubmitting the employee through single touch will ensure their JobKeeper finish flag is now reported and that they no longer continue to show up as eligible on the ATO side.

How Can I Renew or Register for an AUSkey?

AUSkeys have now been replaced by the ATO Machine Credential. The AUSkey service will be closed down on March 27th 2020. Please see here for information on getting a machine credential.

How Can I Check the ATO STP Server Status?

Below are the two web addresses used for Single Touch Payroll in Lightning Payroll.

ATO SBR2 Cloud shows current server status of their main services. PAYEVNT.0003 is the STP service. If it is red, the service is down. Please try again later.

Manage Credentials

The other service required to send STP is the STS/Machine Credential Secure Token Service. Below is an example of how a healthy page would look.

Manage Credentials

What Can I Do if I Forget My Machine Credential Password?

If you have forgotten your machine credential keystore password there is unfortunately no way to reset it. The steps below are how you can most easily test your keystore password outside of Lightning Payroll, and fix the issue if you cannot remember it:

  1.  Log in to RAM on your Lightning Payroll computer using MyGovId, like you did when you first downloaded your machine credential.
  2. Click View or manage authorisations, machine credentials and cloud software notification.
  3. Click on the business/company name (not on 'View') you need the credential for.
  4. Click on Manage Credentials at the top of the screen.

    Manage Credentials

  5. Click Create Machine Credential. If it says Software Required, please see here to learn how to fix the issue.

    Create Machine Credential

  6. Test your keystore password, or change the path and create a new password.

    If you are seeing only one password field, then the ATO's page is detecting the existing keystore file. The location of this file is shown in the keystore path. You can test your password here. If your password is correct a new credential will be inserted into the existing keystore file.

    Ram Single PW

    If you are seeing two password fields, then the ATO's page is not detecting the existing keystore file. The default location of this file is shown in the keystore path. This means you will be creating a new password and a new keystore file.

    Ram Double PW

    The Credential name isn't too important it is up to you. Payroll or Lightning or a name for your computer (so long as it is a single word) is OK.

  7. Tick the box to authorise yourself as the custodian, and download the new credential to the keystore path shown.
  8. If you have additional ABNs which require a credential, you'll need to click back to the RAM homepage and repeat steps 2-7.

Importing a keystore from a manually edited keystore path/filename

If you are using the default ATOMAS/keystore-new.xml filepath, Lightning will automatically detect and use your keystore.

If you have changed the keystore path/filename, you will need to manually import it into Lightning Payroll under Tools >> Import Machine Credential. Click on the blue folder button to browse. Find and double click on the new keystore file, then import to finish the process.

Import credential tools

Import credential select

What Does It Mean If I Get An STP Error Code - CMN.ATO.AUTH.007

If you receive the STP error code CMN.ATO.AUTH.007 it means that the ATO credential used to make this Single Touch submission does not have sufficient permissions.

To increase your credential permissions please contact the ATO or try the instructions below:

  • Login to the ATO Access Manager page.
  • Click on Access and Permissions over to the left.
  • Click on the blue name link for the desired Single Touch Payroll credential.
  • Scroll down the following page and ensure that beside Payroll Event Form (under ATO Transactions) the two boxes are ticked to View and Lodge.
  • Save your changes by clicking Save at the very bottom of the page.
  • Return to Lightning Payroll and resubmit the pay run through Single Touch using your updated permissions under Pays >> Single Touch>> Submit Payroll to ATO >> Create update event.
  • Two minutes later, go into the Single Touch Mailbox and it will check for ATO responses regarding your resubmission.

How Can I Setup Single Touch Payroll?

Doing Single Touch Payroll is easy with Lightning Payroll. Usually you only need to make sure there is an ATO Machine Credential installed on the machine on which you run Lightning Payroll.

If you already have your Machine Credential installed on your computer, you do not need to do anything else to link it to Lightning Payroll directly. Lightning Payroll will automatically find and recognise your Machine Credential.

The only other step is to make sure your Lightning Payroll program is up to date. To do this, click Check for updates now, at the bottom of the Lightning Payroll program. If an update is available, click Yes.

You are now ready to go.

How Do I Process Single Touch Payroll?

From July 2019 the ATO will require that employers align ATO reporting with their pay schedule and submit employee YTD figures using the Single Touch Payroll reporting standard each time pays are made to employees.

The only thing you need to do to be able to send STP in Lightning Payroll is get an ATO machine credential. Please see our FAQ on machine credentials here.

Read the ATO's Single Touch Factsheet

Read our 2018/2019 EOFY Mailer

To process Single Touch Payroll in Lightning Payroll simply complete your pays as usual then click Single Touch >> Submit Payroll to ATO.

To check for Single Touch Payroll response messages from the ATO click Single Touch >> Single Touch Mailbox.

This video tutorial demonstrates how to submit Single Touch Payroll information to the ATO.

How Do I Process End of Year Using Single Touch Payroll?

Note: This method will only work for users who have submitted STP for at least one event throughout the financial year being reported.

Before You Begin

You will require a valid ATO Machine Credential.


Submit STP as usual, by saying yes to the prompt when completing your pay run or by clicking Pays >> Single Touch >> Submit Payroll to the ATO.

The only difference with submitting the last pay of the financial year is to tick the box which says Final pay for the current financial year?

On the next page, you can select your credential, print, preview and submit as normal. That's all there is to it.

If submitting a new event you may find that employees not included in the final pay run are missing. This is normal. If this is the case, we recommend you do a second lap of STP for the final pay run, again making sure to tick the Final pay for the financial year box. This second lap however should be submitted as an Update event, which allows you to send STP for all employees paid within the financial year.

The next pay run will begin your new financial year and all YTD figures will begin again upon the completing of your first July pay run.

ATO Responses:

To check for responses simply go into Single Touch >> Single Touch Mailbox and Lightning will see if anything has been returned from the ATO. Responses take anywhere from two minutes to three days to come back. The program will not recheck until at least two minutes since the last check.

What does the Supplier Not Authorised - CMN.ATO.AUTH.008 Error mean?

If you receive the STP error code CMN.ATO.AUTH.008 it means that the Supplier credential or ABN used to make this Single Touch submission is not authorised to submit on behalf of the client or child company.

Please see our FAQ on submitting STP as a third party for more information.

How Do I Correct Incorrectly Reported JobKeeper Eligibility Dates?

If you have incorrectly reported an employee's JobKeeper eligibility period you may need to correct the STP JobKeeper Fortnight codes as described on the last page of this ATO document, and shown below.

Regarding corrections of these JobKeeper flag codes, the ATO advises:

"This design does not support multiple corrections, so extreme
caution should be taken to ensure accuracy of originally reported
JobKeeper data."

These manual adjustment fortnights can be added into Lightning Payroll under Employees >> Tax Rates >> JobKeeper Settings.

Correct a JobKeeper Start Fortnight

There are several scenarios that may need correction with respect
to the JobKeeper Start Fortnight:

  • Wrong employee – if the wrong employee was reported as
    eligible via the use of the JOBKEEPER-START-FNXX, then
    cancel this employee from eligibility via the use of matching
    JOBKEEPER-FINISH-FNXX where the “XX” fortnights are the
    same (cancellation via matching start/finish fortnights)
  • Incorrect start FN (later) – if a later start fortnight is
    incorrectly reported, report an additional earlier start fortnight.
    ATO will assume the earliest start fortnight is relevant where
    no unmatched finish fortnight is reported. For example:
    reported JOBKEEPER-START-FN02 but should have been
  • Incorrect start FN (earlier) – if an earlier start fortnight is
    incorrectly reported, cancel this entry via a matching finish
    fortnight (cancellation via matching start/finish fortnights) and
    report an additional later start fortnight
  • Future-dated start FN – if the JobKeeper start fortnight is
    greater than the STP Pay Event Pay/Update Date field, then it
    will be ignored, as if not reported. It will only become valid in
    the matching JobKeeper fixed fortnight that applies. Do not
    cancel or otherwise attempt to correct this invalid entry.
    This design does not support multiple corrections, so extreme
    caution should be taken to ensure accuracy of originally reported
    JobKeeper data. This critical detail is used to determine
    reimbursement to the employer.

Correct a JobKeeper Finish Fortnight

There are several scenarios that may need correction with respect
to the JobKeeper Finish Fortnight:

  • Wrong employee – if the wrong employee was reported as
    becoming ineligible via the use of the JOBKEEPER-FINISHFNXX, then cancel this ineligibility via the use of matching
    JOBKEEPER-START-FNXX where the “XX” fortnights are the
    same (cancellation via matching start/finish fortnights)
  • Incorrect finish FN (later) – if a later finish fortnight is
    incorrectly reported, report an additional earlier finish fortnight.
    ATO will assume the earliest finish fortnight is relevant where
    no unmatched start fortnight is reported. For example:
    reported JOBKEEPER-FINISH-FN06 but should have been
  • Incorrect finish FN (earlier) – if an earlier finish fortnight is
    incorrectly reported, cancel this entry via a matching start
    fortnight (cancellation via matching start/finish fortnights) and
    report an additional later finish fortnight
  • Future-dated finish FN – if the JobKeeper finish fortnight is
    greater than the STP Pay Event Pay/Update Date field, then
    this will assist to inform the ATO that the period reported is the
    final pay to be claimed, as the employee becomes ineligible in
    the following fortnight. This is the required timing to report
    cessation of the JobKeeper payment – in the preceding
    fortnight, during the final JobKeeper eligible fortnight. Finish
    fortnights greater than the next JobKeeper fortnight are
    ignored. For example, an employee who becomes ineligible
    on 30/06/2020 will be reported in the pay period covering that
    JobKeeper fortnight (FN07) with JOBKEEPER-FINISH-FN08,
    as the employee may be terminated and not be included in
    future STP reports.

The correction options for the JobKeeper payment are limited,
given the use of the only STP Pay Event field that can be used for
this purpose: Other Allowance Type description field.
No other existing PAYEVNT.2018 field allows for the capture of
this data without delay. Extreme caution should be taken by
employers to ensure that validation and reconciliation processes
are strong enough to warrant confidence in the initially reported

How Do I Get a New Machine Credential On My Second Computer?

If you already have an ATO machine credential file on your PC and need it on a second PC for STP, there are a couple of ways to set it up.

The first way is to reapply for a new machine credential at the ATO's RAM website.

The second is to simply copy the credential file and move it to your new PC using Lightning Payroll's Tools menu at the top of the program.

Click Tools >> Export Machine Credential to save a copy of your ATO keystore XML to a USB or other location of your choice.

Click Tools >> Import Machine Credential to load a machine credential XML file into Lightning Payroll.

For example...
Export the machine credential on the existing STP payroll PC, saving it to a USB. Then transfer the USB to the second PC and use the Import Credential option to locate the XML file on the USB and import it for STP usage on PC #2.

Why is the ATO asking me to provide a software ID?

When contacting the ATO for help regarding Machine Credentials, they may ask you to provide a software ID.

As Lightning Payroll is desktop-based, we do not utilise software IDs for Single Touch Payroll. Desktop-based programs instead utilise locally installed machine credentials (please see the following from the ATO's website).

In cases such as this, you can inform the ATO that you do not have a software ID and simply need advice on how to install your own machine credential.

If this does not resolve the issue, you can also refer them to the following page for further clarification:

How Do I Submit Single Touch as a Supplier or Agent?

Single Touch Payroll messages can be sent from Lightning Payroll under three capacities:

  • Submitting from a company directly (most common, default submission type).
  • Submitting as a Business Intermediary - A business with the authorisation to act on behalf of another business.
  • Submitting as a Registered Agent - such as a BAS agent or a Tax Agent.

If you wish to submit as either a Business Intermediary or as a Registered Agent, simply select Submit as Supplier on the first screen in the STP area (Pays >> Single Touch >> Submit Payroll to the ATO)

Next, select your submission capacity (either Business Intermediary or Registered Agent). Note: Supplier company/agent details must be entered into the program under Settings >> Supplier Information. Agents must include an agent number, Business Intermediaries do not require an agent number.

Submitting as a third party or as a supplier also requires that you are authorised to submit on behalf of your clients. These two different supplier modes mentioned above have two different means of authorising clients.

Registered Agents must add client links for either the BAS role or STP role with the ATO (these authorisations usually already exist) via the Online Services for Agents page.

Business Intermediaries must have the child/client ABN nominate the parent/intermediary ABN for STP authorisations by:

  • Logging into the Access Manager website.
  • Selecting Who has access to my business on the left hand side.
  • Click on Appoint new business and enter the the ABN of the parent/intermediary business to act on their behalf.
  • Press Continue and set the permissions (for STP make sure that the View and Lodge permissions for Payroll Event Form are ticked).
  • Select all and Clear all can be used to select or clear all available permissions.
  • Click Save to preserve the changes.
  • To check that it has worked, log into the Access Manager website as the intermediary/parent company and click on Whose business I can access on the left hand side and confirm your client's business details are displayed.

What Do The Single Touch Button Colours Mean?

The button colour highlights the result of the most recent Single Touch message response.

  • Blue means that this pay currently has no messages sent.
  • Grey means the message has been sent and awaiting response or that a new message has been received and you need to view it.
  • Green means the ATO successfully processed your STP event.
  • Red means there is an unsuccessful or failed STP response message.

Why is Lightning Asking Me For a Location ID?

A Location ID is required by Lightning Payroll for PAYG reporting (STP and End of Year). This value is also known as a PAYG Branch ID. The default value is 1, which means your company has one PAYG Reporting branch.

The ATO states that "A branch is formed where a business entity separately registers its branch to suit the structural, management and accounting arrangements of the organisation. When an entity registers a branch for GST or PAYG purposes, the entity is called the 'parent entity'."

You will need to register with the ATO for additional PAYG branches. See here for more information -

STP Invalid XML Error

If you are receiving an 'Invalid XML Error' when attempting to submit your Single Touch, it usually means that there is an issue with the personal information of the employee named in the error message.

Examples of this include the employee's address being more than 38 characters long or otherwise a non-standard character in the employee's name (such as ö or é).

If you're not able to identify the issue, please go to Settings > Backups and click Send Backup to Support. Please include a brief description of the error. Once you have sent the backup, please give our support team a call on 07 3051 5895.

How Do Amount and Age Thresholds Work for Super?

Before you alter your super calculations, be aware that the automatic 10% superannuation guarantee levy is calculated monthly, not on just one pay period - even if you pay weekly or fortnightly. To correctly double check super calculations you will need to add up all ordinary earnings and all super levy calculations for an entire month before comparing the figures. Running the Super Levy report for the whole month with Show Totals Only unticked is a great way to see what is going on.

Checking the super calculations in only one pay period isn't the right way to go. The reason this occurs is the $450 super threshold (ending 30/6/2022).

Here’s an example:
If David regularly earns $200 per week, he will not be owed super until the third week of the month.
Week 1 Earnings = $200 (has not reached beyond $450 threshold, thus no super owed)
Week 2 Earnings = $200
Month-to-date = $400 (still has not reached beyond $450 threshold, thus no super owed)
Week 3 Earnings = $200
Month-to-date = $600
Having now crossed the $450 threshold for the calendar month, the 10% guarantee is now due to be paid on the $600 earned so far in the month.

Each week to follow in this case would calculate the 10% on that particular pay’s ordinary time amount, as the threshold has now been crossed, and will then reset at the start of every calendar month.

Please note that if Age Threshold setting has also been ticked for a staff member and they're under 18, they must meet the above $450 threshold requirements as well as working at least 30 hours per week, in order to earn super for a period.

What Do I Need To Do With New Super Stapling Changes, and 'Your Future, Your Super'?

From the ATO:

"From 1 November 2021, where new employees do not choose a super fund, most employers will have to check with the ATO if their employee has an existing super account, known as a 'stapled super fund', to pay the employee's super guarantee into."

There is nothing you need to do in Lightning Payroll regarding these changes, but you will need to slightly change your employee onboarding process. Please see here to learn what you need to do differently when setting up a new employee's super, from November 1st, 2021.

Other helpful links:

How Do I Check For Superstream Response Messages?

To check for SuperStream message responses go into the Superstream Mailbox located within the Super Fund Deposits area. Click Check Responses and your program will start to download any message updates, or error details.

If an error response is detected, you'll notice that the original Superstream message will no longer have a status of Sent. It will most likely have changed to Failed, or Progressive. You can find out more information about the error by clicking View beside the message. To get more info, we recommend contacting the super fund directly. It is actually quite rare to receive responses, since super funds are only required to respond when an error has occurred. If everything went through fine your messages are likely to stay in a Sent status. If you are confident that a super payment was successfully received and processed by the fund, you can mark the message as complete yourself.

Does Lightning Payroll Alert When Paying Above the Concessional Super Cap?

Lightning Payroll can warn you before paying above the super concessional cap, to help employees avoid paying excess tax.

From the ATO:

"Concessional contributions are made into your super fund before tax, and include:

  • employer contributions, such as  
    • compulsory employer contributions
    • any additional concessional contributions your employer makes
    • salary sacrifice payments made to your super fund
    • other amounts paid by your employer from your before-tax income to your super fund, such as administration fees and insurance premiums

Once the concessional contributions are in your super fund, they are taxed at the 15% rate. There are caps on the concessional contributions you can make each financial year. If you go over the cap, you may have to pay extra tax."

Lightning Payroll includes a setting to help monitor this cap under Employees >> Super >> Superannuation Contributions >> Alert When Over Concessional Cap? by ticking this box the program will alert you whenever the employee's super has exceeded the cap for a given year.

From 1 July 2017, the concessional contribution cap is $25,000 per year, regardless of your age.

How Do I Edit A Super Funds' Details?

If you need to update a super fund as they have provided a new ABN or USI, you should follow the process to Add A New Super Fund, rather than editing an existing super fund, as you want to have an accurate record of the funds and accounts you've sent messages and money to previously. 

Super funds will not provide you with their up to date bank account details, but rather their current USI (and ABN), which will bring forth their current banking details through the SuperStream network.

Please note that Self Managed Super Funds (SMSF) are treated differently to traditional super funds, and their details can be edited by going to Settings >> Super Fund Providers in the program, and clicking Edit Provider to the right of the line the SMSF is listed in.

How Do I Pay Super in Lightning Payroll?

Superstream is the ATO's superannuation payment standard. Lightning is superstream compliant and allows you to send superstream payment information to Australian super funds.

This brief video tutorial demonstrates how to make Superstream compliant super contributions using Lightning Payroll.

Is Annual Leave Loading Considered Ordinary Time Earnings?

The ATO has recently clarified its position on whether annual leave loading is to be considered ordinary time earnings (OTE), and thus applicable to super guarantee calculations. This categorisation of leave loading as OTE has traditionally been a grey area, where OTE has widely been understood to not include annual leave loading amounts. This clarification of the SGR 2009/2 Super Guarantee Ruling may change what super employees who receive annual leave loading are entitled to.

Why Do Your Staff Get Paid Annual Leave Loading?

Annual leave loading is NOT considered OTE (and NOT to be included within super calculations) whenever it can be demonstrated that it was paid for a notional loss of opportunity to work overtime.

In short, if the loading is paid to replace a missed opportunity at working overtime - it is not OTE (not included in super calculations).

If the loading is applied for some other reason, or you are not able to reasonably show that it makes up for overtime lost - it is OTE (included in super calculations).

How Do I Know Whether Annual Leave Loading Is Paid For Lost Overtime Opportunity?

  • Award or agreement clauses

Some awards, agreements and industries may make this leave loading reasoning apparent, while others may remain silent on why leave loading is paid. In the latter case you should self-assess. For information on awards you should contact Fair Work Australia.

  • Self-assess whether the annual leave loading is or is not OTE

We have introduced a tool to assist you self asses whether or not super on leave loading applies based on an employee's frequency of overtime, found under Tools >> Set Include Leave Loading In Super. This gives you a way to quickly determine - absent any award or agreement evidence mentioned above - whether an employee works overtime on a regular basis.

Past correspondence between the ATO and ICB indicates this is a reasonable way to approach the issue:

"...if an employee is demonstrably working overtime on a permanent regular basis, any annual leave loading that is applicable to that overtime is not considered OTE and therefore no SGC is payable."

In each employee's situation is up to employers to decide, and in some cases a backpayment of super for affected employees may be applicable.

The ATO states that:

"We acknowledge the uncertainty around this topic, and the evidentiary difficulties in identifying the purpose for annual leave loading entitlements. For this reason, we won't apply compliance resources to scrutinise why annual leave loading was paid in previous quarters, where:

  • the employer self-assessed that the annual leave loading was not OTE, with the reasonable position that their annual leave loading was for a notional loss of opportunity to work overtime
  • there is no evidence less than five years old (the statutory period employers are expected to keep records relating to their SG affairs) that suggests the entitlement was for something other than overtime."

Lightning Payroll was released in July 2012 and cannot provide information prior to this.


What are the Due Dates for Super Payments?

The due dates for Superannuation payments can be found here. Usually super needs to be paid by the 28th of the first month following the end of a quarter.

How to Check that You're Setup for Super

To ensure you're completely ready to begin processing super through Lightning Payroll, please ensure the below steps have been followed:

  • Make sure all employees have been linked to a Super Fund:
    • You can link an employee to their chosen fund under Employees > Super > Superannuation fund and clicking the green plus button to add a fund for the employee. If the super fund you wish to link to the employee is not in the drop down list, you will need to add it to the list of super fund providers. Click here for information on how to do this.
    • When linking an employee to a fund, you will need to ensure you have their member number entered correctly
    • If the employee has only one super fund, make sure the box marked 'is Primary Fund?' is ticked. The primary fund is fund where all super levy payments for the employee are to be sent.
  • Make sure that your business bank account details have been entered under Company > Bank Account. Make sure the bank account you will be using to pay the super has been added and is selected under the Bank Account for Super drop down.
    • NOTE: the User ID refers to the ID required by your bank for processing Direct Entry files. To find out what the User ID is, please contact your bank.
  • Make sure your ABN is registered for SuperStream:
    • If it has been more than 2 weeks since you first subscribed to Lightning Payroll and you have only one ABN, you will have already been automatically registered for the SuperStream.
    • If you have more than one ABN or your ABN has changed, you will most likely need to register this new ABN for SuperStream. Do this go, to our website here and login to the Client Login on the top right. You can then add the new or additional ABN under SuperStream Registrations.

How Can I Register for SuperStream?

If you need to register an additional company for SuperStream, you can do this via the client login portal on our website.

Login to the client portal on the top right of the Lightning Payroll website. Once logged in, click on 'SuperStream Registration (Additional Companies)', add the company name and ABN and click 'create'.

Please allow 1 to 2 weeks for your additional company to be registered with SuperStream.

What is a USI?

The Unique Superannuation Identifier (USI) is used in SuperStream to uniquely identify an APRA fund and/or its superannuation product which an employee (member) is contributing to. 

These are kind of like a superannuation product code, required in Lightning Payroll to be able to send SuperStream messages from the program. Your employees will need to provide these USIs to you along with their member information if they are with a typical APRA super fund. They can get a USI by contacting their super fund.

USIs are best entered into the program under Settings >> Super Fund Providers >> Create Super Fund (Online Search).

How Can I Resend SuperStream Messages when the Super Fund/s are Holding the Deposited Funds?

Sometimes you may need to resend the accompanying SuperStream messages for Super Fund deposits that you have already made. This may be due to the messages failing or otherwise not being received by the Super Fund.

To resend messages for deposits you have already paid, you can follow the steps below:

1. Go to the Super Fund Deposits screen and make a note of the 'Deposit Date' of the Super Fund deposits for which you need to resend the messages.

(NOTE: If you cannot see any deposits listed, or you cannot see the correct deposits, you can click 'Show Search Filter' on the bottom left and use the 'Show Deposits by Date' menu on the left. Widen the start and end dates to display more deposits based on when they were created.)

Then, click on the SuperStream Mailbox button. Inside the Mailbox, set the 'dates between' dates to be the same as the 'deposit date' of the deposits that we will be resending the messages for. For example, if the deposit date is the 4th of April, 2019, set the 'Dates Between' to be 04/04/2019 to 04/04/2019

In the box below, you will see the sent messages for your recently created Super Fund deposits.

2. Click View next to the first message that will need to be resent.

3. Then, click Manually Fail on the bottom right of the message information screen and confirm that you wish to fail the message. Finally, hit Finish.

(NOTE: If you are not able to manually fail the message, this means the message is already failed and you can just hit Finish and move on to the next step.)

4. Repeat Steps 2 and 3 for the remaining messages.

5. Once all the original messages have been set to status 'Failed' or 'Manually Failed', click Contributions Report on the bottom right of the Mailbox screen. Make sure the start and end dates are set to the sent date of the original messages. Then, 'select all' and click OK.

A SuperStream contributions report will be generated with each Super fund and their reference ID on each line. Save or print this report.

6. Back in the main Super Fund Deposits page, click on the SuperStream Contribution button.

Under 'Show Deposits by Date', set the date range to once again be the same as the 'deposit date' of the original deposits.

Make sure to click 'Include Paid Deposits'

7. Select all the deposits you wish to resend and then click Next on the bottom right.

8. On this screen, you will be shown the amounts to go to each Super Fund. Click the pencil icon to edit the ABA reference for each fund. Delete the current reference and replace it with the reference ID for that Super Fund from the SuperStream Contributions report you created earlier.

Complete this step for every Fund listed on the screen.

Once completed, click Next again and on the SuperStream Summary page, click Send Messages.

Once the messages have been finished sending, click Finish. You have now successfully resent the SuperStream messages.

How Can I tell If My Superstream Message Was Sent Correctly?

Below is a great way to find out if your Superstream message was successfully sent:

After you have sent your Superstream message/s, go into the Superstream Mailbox. Click Check Responses to refresh the mailbox with the latest message info from the Superstream network. You might not have any responses yet, but don't worry. This is common.

Using the date and message status filter boxes at the top of the mailbox, search for the messages you've just sent.

Click View beside the message you'd like to check.

If your Superstream message was successfully processed by the network, and forwarded to the super fund there will be a value beside Conversation ID. This acts similarly to a tracking number on a parcel and is the unique identifier for that particular message. It can be provided to a super fund if needed.

Why am I Receiving a Failed Validation Error for SuperStream?

If you are attempting to send SuperStream messages and receiving a 'failed validation' error, please check your internet connection.

This error is usually caused by an internet connection problem or otherwise a problem on the SuperStream network end. If your internet connection is functioning, please wait 12-24 hours and try again.

How Can I Add a Self Managed Super Fund

Adding a self managed super fund into Lightning Payroll can be done in Settings > Super Fund Providers.

Click on 'Create Super Fund (SMSF/Manual Entry)' and select 'Self Managed Super Fund' from the Type dropdown.

Note: You may need to input an electronic address. This is used for correctly routing SuperStream messages for the fund. The person with the self managed fund should be able to provide this.

How Do I Get Super Funds' Bank Account Details Into Lightning?

Super funds' individual banking details are brought forth through the SuperStream network using each fund's respective USI. Super funds will no longer give you the bank account details themselves, but rather, will provide you with the USI for the specific type of super fund your employee is registered to within their fund umbrella. Please note that Self-Managed Super Funds are entered differently and do not have a USI.

To bring these banking details forth, you will need to go to Settings >> Super Fund Providers in the program, then click on Create Super Fund (Online Search) and enter the USI you have been provided for the respective fund, and click Next. On the next page, the super fund and all its details should show up with a box to the left of it which will need to be ticked, and you can then click Finish

You will now have the super fund, as well as all of the fund's banking details added to your list of available super funds which can then be attached individually to your staff, along with their member number, via  Employees >> Super >> Superannuation Fund in the program.

It is recommended that you occasionally go into Settings >> Super Fund Providers and click on Populate Fund Data >> Select All >> Next, which will refresh all funds' latest banking information as per the SuperStream Network, as these details can change from time to time from the super funds' end.

How Can I Resend SuperStream Messages and Super Deposits when the Super Fund/s have Returned the Money to my Account?

Sometimes, one or more Super Funds may not be able to match funds you sent to the relevant member. In this situation, once you have received the money back, you will need to send a new message for the deposit and transfer the money again.

To do this, you can follow the steps below:

1. Go to the Super Fund Deposits screen and make a note of the 'Deposit Date' of the Super Fund deposits for which you need to send the money again along with a new message.

(NOTE: If you cannot see any deposits listed, or you cannot see the correct deposits, you can click 'Show Search Filter' on the bottom right and use the 'Show Deposits by Date' menu on the left. Widen the start and end dates to display more deposits based on when they were created.)

Then, click on the SuperStream Mailbox button. Inside the Mailbox, set the 'dates between' dates to be the same as the 'deposit date' of the deposits that we will be resending the messages for. For example, if the deposit date is the 4th of April, 2019, set the 'Dates Between' to be 04/04/2019 to 04/04/2019

In the box below, you will see the sent messages for your recently created Super Fund deposits.

2. Click View next to the first message that will need to be resent.

3. Then, click Manually Fail on the bottom right of the message information screen and confirm that you wish to fail the message. Finally, hit Finish.

(NOTE: If you are not able to manually fail the message, this means the message is already failed and you can just hit Finish and move on to the next step.)

4. Repeat Steps 2 and 3 for any other messages that will need to be sent again to the Super Fund along with the money.

5. Once all the relevant messages have been set to status 'Failed' or 'Manually Failed', click Finish.

6. Back in the main Super Fund Deposits page, click on the SuperStream Contribution button.

Under 'Show Deposits by Date', set the date range to once again be the same as the 'deposit date' of the original deposits.

Make sure to click 'Include Paid Deposits'

7. Select all the deposits that you will be resending the money for. Click Next on the bottom right. You will then be shown a screen confirming the amounts to be sent to each Super Fund.

Once completed, click Next again and on the SuperStream Summary page, click Send Messages.

Once the messages have finished sending, click Direct Entry to create and save a file to upload to your online banking portal later so that you can resend the funds to the relevant Super Funds. Finally, click Finish. You have now successfully resent the SuperStream messages and created a new Direct Entry file ready to upload to your online banking portal to transfer the money.

How Do I Add a Super Fund to Lightning Payroll?

Connect An Employee To An Existing Super Fund

Existing superannuation funds can be connected to your employees under Employees >> Super >> Superannuation Fund and click on the green plus. Clicking the pencil will allow you to edit an existing employee/fund association. You can add more than one fund per employee if you need to. Make sure you tick Is Primary Fund? beside their primary super fund (The fund which will receive all super amounts by default). The Registration Date field can be set to today's date. It simply provides a means of tracking when an employee switches to a different super fund, if they ever do.

Create A New Super Fund

If a super fund you wish to add is not available in the pre-filled list you'll need to create a new super fund under Settings >> Super Fund Providers.

Method 1: Online Search

The Online Search method is the easiest way to add most super funds since all you need to begin is the employee fund's ABN or USI(unique superannuation identifier). Lightning Payroll then uses this information to connect to the ATO's Fund Validation Service and download the related information for any fund/s you've searched for.

You'll then see the search results downloaded from the registered ATO super fund registry. Simply tick the box beside the super fund/s you would like to add to the program and then click Finish.

Method 2: SMSF/Manual Entry

For self managed super funds or non SuperStream compliant funds you will need to set them up manually under Settings >> Super Fund Providers >> Create Super Fund (SMSF/Manual Entry). For major funds the most important information to include is the Fund Name, the ABN and the USI . Lightning Payroll can complete the rest of the fund information (bank details, telephone, etc.) using the Populate Fund Data tool, demonstrated below. You can obtain super fund ABN/USI information from your employees, from the super funds directly, or from the ATO's Super Fund Lookup page .

Self-managed super funds have an electronic address (ESA) instead of a USI.

This example sets up an Australian Super product. Once the primary information has been entered, you can also Populate Fund Data to refesh the fund info against the product USI (non-SMSF funds only).

Select the fund or funds you wish to download details for and click Next.

If the ABN and USI are correct, the ATO's fund validation service should locate details and they'll be displayed in the upper box. If no extra details were found, the previously selected fund appears in the lower box. Click Finish and the chosen fund profiles - formerly only partly complete - now include extra information.

Once you've created the fund just remember to attach it to relevant employees under Employees >> Super >> Superannuation Fund >> Add Super Provider by marking the fund as Primary.

How Can I Delete Unused Super Funds?

You might not be able to delete an unused super fund if it is still connected to an employee or an old deposit, but here's how you can at least make it Inactive and get it out of the way.

  • Go to Settings >> Super Fund Providers.
  • Click Edit Provider beside a fund you wish to get rid of.
  • Set the type to Non-compliant Super Fund.
  • Enter a fake ABN of 10000000000, which is the number one followed by ten zeroes.
  • Untick the Active? box at the bottom.
  • Save the changes. The unused fund is now hidden.

To view your hidden/inactive super funds, tick the Show Inactive? box at the bottom of Settings >> Super Fund Providers.

Can I Submit TFN Declarations in Lightning Payroll?

TFN Declarations do need to be completed by your employees, however they do not need to be sent into the ATO since Single Touch Payroll reports all of the relevant tax coding to the ATO with each submission.

Make sure to configure the employee's tax settings accordingly as per their TFN dec, under Employees >> Tax Rates and this information will be reported along with Single Touch Payroll.

How Can I Enter Employee Reportable Fringe Benefits?

If you would like to enter Reportable Fringe Benefits for an employee, you can do this in Employees >> Tax Rates >> Reportable Fringe Benefits.

To add in benefits for a particular financial year, click the pencil icon on the right hand side for the relevant financial year.

In this next screen, you can also set Fringe Benefit Tax exemptions for the employee for the selected financial year.

Why is Lightning Payroll Calculating So Much Tax for One Employee?

The most common reason why an employee is being overtaxed is an incorrect Tax File Number. Lightning Payroll uses an Australian Tax File Number validation system which is checked in real-time by simply entering a TFN into an employee’s Tax Rates screen. If the TFN displays in green, it is valid. If the number shows up in red, it is invalid (seen below).

If you find the TFN you’ve been given is invalid please ask your employee to verify their correct TFN.

See here for more information on temporary TFNs.

What Do I Do If My Employee Doesn't Have a Tax File Number?

If your employee does not have a Tax File Number (TFN) or has not yet provided you with one, there are a number of general TFNs that can be utilised in Lightning Payroll.

The ATO provides a list of general TFNs here and you can choose which one to use depending based on the circumstances. Make sure to read the details for each general TFN to ensure you choose an appropriate option.

Depending on the situation, there may not be a general TFN that fits the specific circumstances. If so, contact the ATO on 13 28 61 for more information.

TFN code numbers and when to use them

TFN code number

When to use code number


Use if the payee has not provided a TFN, or fails to provide one within 14 days. Taxed at full rate.


Use if you receive a declaration from the payee which says they have applied for a TFN.

This code should be updated with the payee’s TFN, or, with the no TFN quoted code when the payee fails to provide the TFN to the payer within the 28 day period allowed.


Use if a payee is under 18 years old and claims the general exemption because they do not not earn enough for tax to be deducted.

If circumstances change and the payee subsequently earns a level of income that attracts tax, a TFN will be required to be provided at that time.


Use if the payee is a recipient of a social security or service pension or benefit (other than Newstart, sickness allowance, special benefits or partner allowance) an exemption from quoting a TFN may be claimed.


Use if alphabetic characters appear in a TFN.

How Do I Update To The Latest Tax Tables?

Lightning Payroll has the ability to calculate tax on pays from the 2013 financial year through to the current financial year. Each June we release an update which includes any tax changes for the approaching financial year.

Lightning Payroll versions 2020.1.1 and above include the latest changes to ATO PAYG tax tables.

The best way to tell that you're using the current financial year's tax tables is to check the first number of your software's version number (I.e. 2020.1.1) . Your version number is shown at the bottom of the Lightning Payroll program window.

The best way to update is by clicking Check for updates now? at the bottom of your program. Click here to find out more on how to update your software.

To view public tax tables for the current financial year, you can visit the ATO here -

Where Do I Enable HECS/HELP/TSL?

To enable HECS, HELP or TSL withholding for an employee you need to go into the Employees >> Tax Rates screen and tick the appropriate box beside that employee's name.

How Do I Set Up Tax for Employees on a Working Holiday?

From 1 January 2017 employers will need to register with the ATO to be able to tax staff using the working holiday tax table rates. Once your company has registered you will be able to apply the working holiday tax scale to applicable employees within Lightning Payroll under Employees >> Tax Rates >> Special Tax Rates >> Working Holiday Tax Scale >> Use Working Holiday Tax Scale.

We've also added a report to help keep track of working holiday pays under Reports >> Tax >> Working holiday tax scale summary. This helps show which tax scale has been applied to each of your employees' pays.

Why Am I Getting A Timeclock Server Connection Error?

Some Android Timeclock users are encountering errors when connecting to our server since late September 2021. This is fixed by updating your Android version higher than Android version 7.1.

The issue is due to an expiring certificate within Android, explained here -

To learn how to check your version number or to update, please visit the Google Support page here -

How Do Employees Use Timesheets in the Online Portal?

Please note, that in order for your employees to use timesheets, you will need to first ensure they are set up in the Online Portal with timesheets enabled. Please see our FAQ here on setting up Online Portal. You will then need to set up shifts, please see our FAQ here on setting up shifts in Lightning Payroll.

Employees will see the following screen when they login to the Employee Login via our website; they should then navigate to the Timesheet tab.

Timesheet Portal Main Screen

The search filters on this page allows employees to see shifts already submitted between the dates entered. Changing these dates to the employee's pay run dates - Monday 01/03/21 - Sunday 07/03/21, for example - will allow the employee to see if they have already submitted shifts for that pay run. 

To add a new shift to their timesheets, employees should click the New Shift button, and select the type of shift they wish to enter hours against, using the drop-down list, as per the following example.

Timesheet Portal Main Screen

This screen then allows employees to edit the date and duration of the shift, like you can see in the below example. Once all fields are completed, click Save Shift, and this shift will now be available to sync into the Pays screen of Lightning Payroll. 

Timesheet Portal Main Screen

Employees will also now see any saved shifts within the search filter dates input on the main Timesheet tab in the Online Portal. As you can see below, employees are able to Edit or Delete the shifts they have saved.

Timesheet Portal Main Screen

Saved shifts will now be availble for the payroll officer to sync into the Pays tab of Lightning Payroll, for more efficient processing of pays.

How Can I Setup the Online Employee Portal?

The online employee portal allows employees to add or adjust their contact and bank account details, request leave, submit time sheets and clock in and out of available shifts independently using the timeclock.

For leave requests please see our other FAQ on the topic.

Once activated, employees can access their personal portal by visiting the Lightning Payroll website and clicking Employee Login on the top right.

Before activating a portal account for an employee, make sure the employee's email address has been added under Employees > Details > Personal.

The portal can be activated for a selected employee in Employees >> Details >> Online Portal.

portal settings

Clicking Activate will allow you to begin selecting what features of the portal the employee can use.

Personal Details - Selecting this will allow the employee to update their contact details and time clock pin (if the employee uses the LP timeclock app on Android devices)

Bank Account Details - Selecting this will allow the employee to add, edit or delete bank account details for receiving their pay. The employee can also specify if they wish to have their pay split between multiple accounts automatically.

Any changes the employee makes to their personal or bank details in the portal will be automatically synced to Lightning Payroll the next time the program is reopened


Manual Time Entry

This is where you can select whether the employee can clock in and out of available shifts or add and edit time sheet entries via the online portal. To activate this, you will first need to ensure you have created shifts and assigned them to the relevant employee.

Allow Employee to Clock In and Out Through the Timeclock? - Selecting this option will allow the employee to clock in and out of selected available shifts directly via the portal. Clock in and out data entered by the employee can then be synced directly to the employee's pay in Lightning Payroll.

Allow Employee to Manually Edit Their Timesheet? - Selecting this option will allow the employee to manually edit their start and end times for selected available shifts. Timesheet data entered by the employee can then be synced directly to the employee's pay in Lightning Payroll.

Completing Activation

When you are satisfied with the settings, click Refresh Employee Portal to complete the portal activation process. The employee will receive an email with details on how to log in.

Activate Multiple Employee Portals

The employee portal can be setup and activated for each employee individually, however, if you wish to have multiple employees use the portal with the same settings applied, you can use Configure Multiple Employee Portal Settings under the Tools menu.

How Do I Use the Lightning Payroll Timeclock App?

Lightning Payroll includes a mobile Timeclock app for Android devices (Android version 4.4 and above) which can provide a way for you to precisely record when employees start and finish work. All hours and shifts recorded in the Lighting Payroll app can then be downloaded/synced with the Lightning Payroll Pays screen, filling out pays in seconds.

Please click here for related shifts and rosters information.

Download & Installation

The first thing you’ll need to do is download the Lightning Payroll Android App on the Android device or devices you wish to use as a Lightning Payroll timeclock. To download the LP Timeclock, head over to the Google Play Store and follow the prompts to install the app. Updates will then be handled through Google Play.

Get it on Google Play

Connect Your Android LP Timeclock to Lightning Payroll

When you open the Android LP Timeclock app for the first time it will ask you to enter your Lightning Payroll subscription details and to login. This will connect the Android device to your Lightning Payroll account. If you are unsure of your account login details, they can be found inside Lightning Payroll under Tools >> Licence Details.

When you first login your device will show you the Not Authorised screen, since it still needs to be authorised from the other side, within your Lightning Payroll software. Once authorised you will be able to view company and employee data and begin clocking in and out of shifts.

To authorise the Android device, open Lightning Payroll and go into Company >> Timeclock Devices and click Check For Devices.

The device will then appear, and allow you to give it a nickname for easy recognition and to set it to Active, confirming its connection to the company you are editing. To save the authorisation, click Send Updated Employee Data, and you should see a confirmation message.

To update the newly authorised Android device, click the Refresh button at the bottom of the Not Authorised screen, or restart the app.

Clocking In and Clocking Out

Now that the device has been connected to your Lightning Payroll software, you're ready to go. The LP Timeclock app has been designed to be used on any number of devices that you wish to connect to your company. Ideally it would be used on a single device for all employees to share, but it is flexible enough to be installed on each employee's device if it needs to be used off-site.

If you are using the device as a timeclock for more than one company, you will see a company selection screen by default. For most users however, only a single company will be connected to the device, so the employee selection screen will be the default home screen. To clock in, an employee just needs to tap their name and enter their timeclock pin.

Their Timeclock PIN is a four digit number which is set to 1234 by default, but can be changed for each employee inside Lightning Payroll under Employees >> Details >> Timeclock Pin.

Note: If you make any changes to an employee, their shifts or their Timeclock Pin, you will need to got into Company >> Shifts and click Send Updated Employee Data to update the device. Restarting Lightning Payroll refreshes devices automatically.

Once the pin has been accepted, you will either a list of their shifts, or an error screen advising that they have no shifts set up yet.

If no shifts are visible, then you will need to set them up in Lightning Payroll under Company >> Shifts as demonstrated in our related FAQ.

If all is well, their associated shifts will be shown. The employee can then select the appropriate shift that they'd like to clock into.

They'll then be instantly clocked in. Press OK to be returned to the beginning.

Clocking out is achieved by repeating the process. The employee must select their name from the list, and enter their four digit Timeclock PIN. They will then see the shift they are currently clocked into.

Press the Clock Out button to clock out.

Importing Timeclock Data Into Your Payroll

The most important part of the process is the importing of the timeclock data into your pay run. This is done in Lightning Payroll under Pays, using the Timeclock Sync button.

The Timeclock Sync window shows any completed timeclock shifts that are available for importing into the current pay run. You can set these shifts to round up, down or two the nearest minute, five minutes, etc. if you like.

The tickbox to Include Unrostered Shifts allows you to import shifts into your Pays without having to have those shifts pre-scheduled within the Rosters screen, as described in our related FAQ. Importing an unrostered, timeclock shift will automatically create a rostered shift which is what the Pays screen uses to gather worked hours, allowances, and pay rates from.

For raw timeclock information, including details on all shifts currently underway, their is a timeclock report. This report can be found under Reports >> Timeclock.

What Generates An Employee Portal Account and Email?

When activating the online employee portal for the first time an employee will be notified by email of their username and password.

To trigger the email make sure to first activate the employee with the tickbox and then click Refresh Employee Portal under Employees >> Details >> Online Portal.

Employee Portal Activate

You should see a notification on screen which looks something like this:

Employee Portal Created

The employee will receive an email like this, which includes their username and password. They can then use these details to login to our Employee Login page here. It is recommended that they change their password upon logging in.

Employee Portal Email

The other time an employee might receive an account email is when their name is changed. The reason for this is that their username/login will change since it is based on their full name.

Why Am I Getting An Error After Agreeing To The Update?

 If you are encountering an 'Access is denied' error like the one shown below when updating, it is caused by a false positive or false alarm in your security software. Some security applications, particularly Trend Micro or Symantec can prevent Lightning Payroll from applying updates to itself on your PC. Our updates are totally safe.

We build and publish the program with the highest standard of code signing available (Extended Validation). Please ensure you keep your security software up to date. On occasion you may need to manually configure it and make an exception for Lightning Payroll to properly function.

Norton users click here for instructions on unblocking Lightning Payroll, if it has been blocked.

Trend Micro Update Blocked Alert

A quick, short-term fix is to temporarily disable Trend Micro then run the LP update again. You can disable Trend Micro by right-clicking the Trend Micro icon in the Windows system Tray, then untick the option which says Protection Against Viruses & Spyware.

Trend Micro Update Blocked Alert

The long term fix is to follow the steps below.

LP Update Alert

After agreeing to a Lightning Payroll update, you may see this notification in the lower right hand side of your screen. If you do not see the Spyware Removed notification below, you likely have Trend in Mute Mode. You can disable mute mode in the Windows system tray, by right-clicking the Trend Micro icon and unticking the Start Mute Mode icon.

Click on More details...

Trend Micro Update Blocked Alert Notification

Next, highlight the infected file on the left and click Restore.

Trend Micro Restore Script

Finally, confirm the restoration of the update script by clicking Yes. This will allow Lightning Payroll to update itself in future, without you having to disable Trend Micro protection. In some cases this process must be repeated a second time before the exception sticks.

To continue updating Lightning Payroll you will just need to restart the software and answer yes to the update question once again. Trend should no longer prevent the update.

Trend Micro Restore Script

Why Does Lightning Payroll Say My Version Is Up To Date When It Is Not?

If your Windows computer is not kept up-to-date with the latest updates you may encounter an issue with Lightning Payroll's automatic updates. This is due to older Windows systems using outdated root certificates, used for HTTPS/SSL web traffic. Our automatic update server is using renewed certificates which outdated Windows versions cannot communicate with, such as the very common, two year old Windows 10 release number 19041.

Your Lightning Payroll should be at least version 2022.3.2p5. If your version number is less than this and Lightning Payroll says incorrectly that You're up to date (since it cannot detect newer server updates) then you will need to either:

Why Has Lightning Payroll been Quarantined by Anti-Virus?

Sometimes Lightning Payroll may be attacked or misclassified as spyware by your security software. This can happen and is known as a false positive.

We build and publish the program with the highest standard of code signing available. That's all that can be done from this end. Please ensure you keep your security software up to date. On occasion you may need to manually configure it and make an exception for Lightning Payroll to properly function.

If Lightning Payroll is mistakenly quarantined by AVG or Avast, you will see the below notification appear on your screen. Click 'Show Details' and then select 'Open Quarantine'.

In the quarantine folder, select the files identified as Lightning Payroll (see circle) and then click 'Restore and Add Exception' on the bottom right.

You will now be able to run Lightning Payroll. If the shortcut has disappeared from your Desktop, please go to 'Type hear to search' menu on the bottom left of your desktop and search for Lightning Payroll.

The Lightning Payroll app should show up under Best Match. Right click on the app and select 'pin to taskbar'.

You will then be able to run Lightning Payroll from the taskbar.

What Does 'Failed to execute script payroll' Mean?

If Lightning Payroll says 'Failed to execute script payroll', then the program has been reinstalled while it was still running in the background.

To fix this error, please restart your computer, then reinstall the program again using the appropriate link for your computer below.

Windows Users (Win 7 and newer) -

Mac Users (Sierra and newer) -

If the error persists. please try disabling your security software, then try again. If your security software is out-of-date or failing it will flag our safe installer and prevent a clean installation.

Why Can't I Put My Licence On Another Computer?

Any annual Lightning Payroll subscription allows you to unlock and use the program on two computers at any one time. This limit is fixed per subscription and is not able to be raised.

If Lightning Payroll is giving you either of the following errors you will need to clear one or both of your two allowed seats from the current licence/subscription.

Older Versions Max-Seats-Error

Old registered seats exceeded error

Newer Versions Max-Seats-Error

New registered seats exceeded error

Note: Removing the licence from Lightning Payroll does not affect your pay data or your program installation at all. It will simply lock your application soon after removal, putting Lightning Payroll into a read only state until an active licence is again provided.

There are three ways to fix this error:

  1. Removing the installed licence from an existing Lightning Payroll installation at the top of the program under Tools >> Licence Details >> Remove System. Remove system button
  2. Sometimes the old system has crashed and you cannot open the program. In this case you should log into your client account here on our website and go into your subscriptions. Here you can release the seats for any of your subscriptions. This will free up both seats of your subscription for you to then reenter as needed. My subscriptionsRelease seats
  3. Contact our support team and we can reset your seats for you.

Why Am I Getting A Database Load Error?

If you encounter an error opening the program about being 'unable to connect to the database' or 'unable to load the database' it is often fixed by following the steps below:

1) Please download and run our small utility program to tidy your Lightning Payroll data folder. It should launch your program after that.

2) If the problem continues, please try uninstalling and reinstalling the program using one of the Download Free Trial links at the top of this page. Your data is not affected by this process.

3) If it still fails after this, please contact our support team.

Why Can't I Open Lightning Payroll?

If you receive the following error message 'failed to execute script payroll' when trying to open Lightning Payroll, you can resolve this by restarting your computer and reinstalling the program. This solution is fairly simple and reliable however, and best of all your pay data is safe and won't go anywhere.

Restart your computer first and then download and reinstall Lightning Payroll from here (Windows XP and above).

Restart your computer first and then download and reinstall Lightning Payroll from here (Mac OSX versions 10.11 and above).

DLL Error Message (Windows 7 and Windows 8 users only)

Some users on WIndows systems may get a DLL related error when opening the reinstalled application. This can often be fixed by installing the latest Visual C++ Microsoft package, required by newer versions of Lightning Payroll. If this fails and DLL errors continue, please update your Windows in your system settings to the latest version of your particular OS. Lightning Payroll is compatible with the latest versions of Windows 7, 8 and 10.

Another Possible Windows Startup Issue - User Account Privileges

Some Windows users can encounter issues when opening Lightning Payroll due to insufficient privileges on their Windows User Account. Lightning Payroll requires Administrator privileges to function fully.

While uninstalling and reinstalling Lightning Payroll is a reliable fix if the program is not opening, this issue is commonly related to user rights. Simply running Lightning Payroll as Administrator may fix the issue. Please see below for info on how to run Lightning Payroll as admin.

To run Lightning Payroll as administrator simply right-click the Lightning Payroll shortcut on your desktop or taskbar and then click 'Run as Administrator'. This can look a little different depending on your version of Windows, and on Windows 10 you'll have to right click the shortcut, and then also right click on Lightning Payroll within the shortcut.

Why Can't I Open the Installer File I Have Just Downloaded?

If you have downloaded the program and see the warning Windows has protected your PC this is a false alarm which can happen from time to time as we are required to renew security certificates used to codesign Lightning Payroll. This warning goes away with time, once Microsoft recognises the new certificate belongs to us.

To continue, simply click More info >> Run anyway.

Note: Benon Technologies Pty Ltd is the correct, verified publisher of Lightning Payroll, based in Brisbane, QLD as seen in the pictures below.


Windows Smartscreen One

Windows Smartscreen Two

Why is Lightning Payroll Not Displaying Correctly?

If you are using a Windows device with an ultra-high resolution screen (e.g Microsoft Surface) or monitor you may experience display issues with Lightning Payroll, we have found the following solution to be quite helpful:

  • Right click on the Lightning Payroll shortcut on your desktop.
  • Select Properties.
  • Go to the Compatibility tab.
  • Click Change high DPI settings.
  • Tick Override high DPI scaling behaviour and then select System (Enhanced) below.
  • Click OK and then Click Apply.

This solution will allow Lightning Payroll to be displayed correctly without having to adjust your resolution and will not affect any other programs.

How Do I Contact Your Support Team?

Our support team can be reached on 07 3051 5895 or by email at from 8am to 4:30pm Monday to Friday (QLD Time, excluding public holidays).

Why Does Lightning Payroll Keep Updating to the Same Version?

If you are attempting to update Lightning Payroll to the latest version but after each update you find yourself on the same version as before, there are two options to fix this:


Option 1 (Windows Only)

  • Close down the Lightning Payroll program.
  • Click here to download this file (local_updates_delete.bat).
  • Open the file from your PC and it should delete the broken Lightning Payroll update (It may trigger warnings which you may have to override, but this file is certainly safe).
  • Go back in to Lightning Payroll and click Check for Updates Now? at the bottom of the screen.

If this fails, please download and reinstall the full application using this link, or try option 2 below.


Option 2 (Windows and Mac)


  • Close down the Lightning Payroll program.
  • On your keyboard, press the key with the windows icon + R  at the sametime.
  • In the dialog box that opens up, type in %localappdata% and click OK.
  • In the new window that opens up, double click on the Lightning Payroll folder.
  • Double click on the folder named updates
  • Delete the two folders named frozen and prepared
  • Go back in to Lightning Payroll and click Check for Updates Now? at the bottom of the screen.

If this fails, please download and reinstall the full application for Windows using this link.


  • Close down the Lightning Payroll program.
  • Click on Finder and then on the top left select Go and then Go To Folder.
  • In the dialog box, type ~/.LightningPayroll/updates and click Go
  • Drag the two folders named frozen and prepared to the trash.
  • Go back in to Lightning Payroll and click Check for Updates Now? at the bottom of the screen.

If this fails, please download and reinstall the full application for Mac using this link.

Why is an Employee 'Locked'?

If you are trying to edit a past pay in the Pays screen, these are usually locked/unlocked using the padlock button at the bottom of the edit pay window.

If however, you ever see one or more employees listed as Locked under Employees, it is usually due to a licence issue.

If only some of your employees are listed as Locked then you are exceeding the allowed number of employees for your current licence tier, and will likely need to upgrade.

To check the expiration date or the employee limit of your currently installed licence/subscription, go to Tools >> Licence Details .

Note: Sometimes terminated staff affect the limit if they've been left active within the program. Click here to learn how to terminate . If all terminations have been kept up-to-date and you still can't pay all the staff you need to, you'll just need to upgrade to the next licence tier.

If all employees are listed as Locked then the program does not detect a valid licence/subscription at all. This means you'll be in 'read-only' mode and will only be able to do things like view and print information, but not add employees or enter pays. Perhaps it has expired, or you're yet to enter the new subscription ID number which gets emailed through each year following payment under Tools >> Licence Assistant.

Why Might I Be Getting Email Errors?

There are a number of reasons why you might be receiving email errors.

We recommend you go to Company > Email and click Send a test email to help diagnose the problem.

Most email errors (such as a socket error) are due to incorrect or missing SMTP server settings. You'll need to check with your email provider to ensure you have the correct Server Name, Port and Encryption details in Company > Email > SMTP Server Settings.

If the error message you receive mentions a 'username/password' or 'authentication' error, you need to ensure the correct username and password for the email account are entered. Again, you can get these from your email provider.

'Database is at a Newer Version' Error?

This error usually occurs when restoring a new backup into an older version of the software

Please download and reinstall from the appropriate link below to fix the error.

Download for Windows (Windows 7 and above)

Download for Mac OSX (Version 10.11 and above)

LP Virtual Assistant