Paying Super
You pay super from each pay run, so the super for a pay period goes to the funds with the same staff, amounts and payment date. Microkeeper prepares a super submission from the pay run's payslips and sends it to Beam, the super clearing house. Beam takes the total from your bank account by direct debit and pays each employee's fund.
| Required plan | All plans |
|---|---|
| Required access | Payroll - Full Access, for the pay cycle |
Navigate to Menu > Payroll > Payruns, click View on the pay run, then Complete Payrun and 4. Pay Super.
Before you pay super
- Super is set up: you've signed up to Beam and verified the bank account super is paid from. See Set Up Super.
- The pay run is complete, and its Payment Date is right.
- Each employee's details are complete: super fund and member number, tax file number, date of birth, gender and address.
Prepare a super submission
- Click New Super Submission.
- Check the bank account, pay cycle, pay run, pay period and payment date.
- Choose the staff:
- All staff (Recommended): everyone in the pay run.
- Staff without errors: leaves out staff with errors to fix, so you can pay the rest now.
- Manually select staff: choose who to include.
- Click Prepare Super Report.
Check the Super Contribution Report
The report lists each fund's members with their Account Number (member number), date of birth and each kind of super: Employer, Additional Employer, Salary Sacrifice and After Tax Member. Total for all super funds is the amount Beam will debit. Click Export CSV to keep a copy.
Fix errors before paying super
If anything is missing, the report shows These errors must be actioned before super can be processed with each error. Fix them, then click Refresh.
| Error | Fix it in |
|---|---|
| Member number missing | The employee's Super Fund Details, or ask them to finish Super Setup. A member number shows in red as TBA |
| Super fund missing | The employee's Super Fund Details |
| Gender missing, TFN not valid | The employee's profile |
| Your business bank account must be verified to process super | Bank Details. See Set Up Super |
Pay the super
- Click Submit Super. The payment gateway shows the bank account and Super to be paid.
- Type the same amount in Enter amount to confirm.
- Click Reviewed. Microkeeper checks the submission with Beam.
- If it's valid, you'll see Data Valid, and that the funds will be debited within 1 to 5 days by Precision Administration Services, which runs Beam. Click Pay Super.
The payment shows in the Process Log. If Beam finds a problem, it's listed instead: fix it and submit again. Beam can also list warnings, such as an employee's missing phone number. They don't stop you paying super, but fix them on the employee's profile.
If you've already paid super for this pay run and staff, Microkeeper warns you. Only tick I wish to bypass duplicate detection if you mean to pay it again.
If no super is due for the pay run, the report says "No super is payable for this pay run." Click Record no super payable to mark it done.
Track a super payment in the Process Log
The Process Log tab lists each super payment for the pay run: who submitted it and when, the period, the staff, the total and its status.
| Status | What it means |
|---|---|
| Received | Beam has the super data |
| Waiting | Beam is waiting for the direct debit, which can take up to 2 business days |
| Clearing | The payment is in, and clearing |
| Paid | The payment has cleared, and is being paid to the funds |
| Processed | Every fund has been paid |
| Partial | Paid, but one or more funds refunded a contribution. See the Refunds / Skipped tab |
| Duplicate | A matching payment was already made |
| Failed | The super data didn't go through. Check the messages, fix the problem and submit again |
| Dishonoured | The direct debit didn't go through. Check the bank details and funds, then submit again |
| Refunded | Beam couldn't pay the funds, and refunded the money to your account |
| Cancelled | The payment was cancelled |
To see exactly what was sent, click the three dots on a payment and choose View Audit Report.
Cancel a super payment
A payment can be cancelled until it's past Waiting. In the Process Log, click the three dots on it and choose Cancel Contribution.
Check member numbers sent back by funds
The Members tab lists the member numbers funds sent back for staff in the pay run, with the fund's USI and what Microkeeper did. A member number is saved to the employee's profile when the fund matches their current fund. If it doesn't, click the employee to check their Super Fund Details.
Redo refunded or skipped super
The Refunds / Skipped tab lists super a fund refunded, and staff left out of a payment. Each one has its message, so you can fix the employee's fund details first.
- Fix the employee's details, such as their fund or member number.
- Tick the payments to redo, and click Redo Selected.
- Check the report, then pay it as usual.
Staff left out with Staff without errors are listed from 24 July 2026. For a payment before then, pay them with Manually select staff.
See every super payment for the year
Navigate to Menu > Payroll > Super for every super payment in a financial year, across all pay runs. Choose the ABN, then the financial year, and Successful, Failed or All. Click a payment's pay run to open its Pay Super.
