Answer
Yes. You can use an external clearing house or SuperStream gateway for Payday Super if you prefer. Lightning Payroll supports this by preparing a SuperStream Alternative File Format (SAFF) file that can be uploaded to many third-party providers.
For ordinary processing, still start from Pays >> Payday Super. The SAFF option changes who sends the SuperStream messages and handles the final payment after Lightning Payroll has prepared the contribution data.
If you previously used the ATO's Small Business Superannuation Clearing House (SBSCH), note that it closed permanently from 1 July 2026 as part of the Payday Super reform — its quarterly design does not support the more frequent contribution schedule Payday Super requires. Choose a commercial clearing house or SuperStream gateway that accepts a SAFF file instead, or use one of Lightning Payroll's built-in payment methods above. See the ATO's guidance on transitioning from the SBSCH for more detail.
You Still Need A Primary Fund For Each Employee
Even when an external clearing house sends the contributions and makes the payment, keep each employee's primary super fund set under Employees >> Super >> Superannuation Fund, and still create the super fund deposits in Lightning Payroll.
The reason is the payslip. The fund name and the employee's member number are printed on the payslip from the primary fund, and the line confirming that a payment was made to the fund, along with its date, comes from the super fund deposit. Without a primary fund the payslip can only say that a superannuation payment has been noted for payment, with no fund name and no member number.
Australian payslip rules require super contribution details to be shown. See the Fair Work Ombudsman's Pay slips page for what has to appear.
Export A SAFF File For A Payday Super Batch
- Go to Pays.
- Complete the pay run as usual.
- Click Payday Super.
- Select the pays to include and resolve any validation warnings.
- Click Create.
- Review the super amounts, funds, employee details and member numbers.
- On the SuperStream Summary, click Need a manual SAFF file export? instead of sending messages directly through Lightning Payroll.
- Save the generated CSV file.
- Upload the CSV to your chosen clearing house or gateway and complete their payment process.
Important Timing Notes
From 1 July 2026, contributions generally need to be received by the employee super fund within 7 business days after payday, unless an ATO exception applies. If you use an external provider, allow time for their upload checks, validation queue, payment processing and fund allocation.
The Super Fund Deposits screen may still be used to search the created deposit or follow up on a SAFF batch, but it should not be used as the normal starting point for a new Payday Super contribution.
If you are new to Payday Super, see How can I handle Payday Super in Lightning Payroll?
For other payment options, see What SuperStream payment options are available for Payday Super?
