Answer
Before you lodge a Single Touch Payroll submission, Lightning Payroll may show a Single Touch Payroll Super Liability warning. It appears when an employee's year-to-date super liability reported to the ATO is higher than the year-to-date super calculated on their pays. The same message appears in Pays >> Payday Super.
This is a warning only. It does not stop you lodging, and it does not change your pays or the figures sent to the ATO.
Why the two figures can differ
From 1 July 2026 the super liability reported through STP must be at least the super guarantee rate (12%) of the employee's qualifying earnings. Lightning Payroll has reported it this way since that date. Super on each pay is still calculated from the settings on the employee and the pay, so the two figures differ when:
- A bonus or commission was paid without being included in super calculations. The ATO counts most bonuses as qualifying earnings, so the bonus raises the reported liability even though no super was calculated on it.
- The employee's compulsory super rate is set below the current super guarantee rate.
The warning names the employee and shows the reported amount, the amount calculated on pays and the difference. For an excluded bonus, the difference is 12% of the bonus.
Is super payable on a bonus?
In most cases, yes. The ATO treats a bonus as ordinary time earnings and qualifying earnings unless it is paid solely for overtime or other work outside ordinary hours. A bonus that is at least partly a reward for ordinary work, such as a performance bonus, is included in full. See the ATO page What Payments Are Qualifying Earnings? and our FAQ What Are the ATO's Qualifying Earnings Rules for Super?
Bonuses marked as Director's Fees or as a Return to Work payment are not counted as qualifying earnings in Lightning Payroll.
Please note: Lightning Payroll cannot advise whether a particular payment is exempt. If you believe super is not payable on a bonus, confirm this with your accountant or the ATO.
How to fix it when super is owed on a bonus
- Open the pay run that contains the bonus and click the pencil to edit the employee's pay.
- Click Edit to the right of Bonus/Commission on the Edit Pay screen.
- Open the bonus, tick Included In Super Calculations? and save.
- Check that the super on the pay has increased by the difference shown in the warning, then save the pay.
- Pay the extra super to the employee's fund as soon as possible.
- Lodge your next STP submission as normal. The warning no longer appears once the super calculated on pays matches the reported liability.
For more on entering and editing bonuses, see Where Can I Enter a Bonus or Other Irregular Gross Payment?
If the cause is a compulsory super rate below the super guarantee rate, correct the rate in the employee's super settings and speak to your accountant about any shortfall on pays already made.
If super is not owed
You can continue and lodge. Because the reported liability is a year-to-date figure, the warning will keep appearing for that employee on each submission until the end of the financial year.
