Payruns page show unpaid Super for several months but is all paid on time, No unpaid Super

Hi Heidi789​ 

Thanks for the background and for having your SBSCH payment records on hand.

To explain how this works: AccountRight's Superannuation Payments report only reflects super paid through MYOB's own Pay Super feature. It has no visibility of payments made through external channels — the SBSCH, a third-party clearing house, or directly to a fund — so any liability paid that way will continue to show as Unpaid in MYOB until it's reconciled in your file. This isn't a defect; it's a function of the payment happening outside MYOB entirely, the same way MYOB wouldn't know if you'd paid an invoice by handing someone cash.

Here's what to do to clear the September quarter correctly:

1. Reconcile your super liability account in MYOB to confirm which periods were paid via SBSCH and which, if any, are genuinely outstanding.
2. Record that payment against the liability manually, rather than through Pay Super. Running it through Pay Super risks submitting a batch that includes a period already paid elsewhere, which can result in a double payment to the fund.
3. We'd recommend switching to MYOB Pay Super so you have automatic visibility of your payments going forward. If and when you make that move, confirm your cut-off date with whichever method you're currently using, so there's no overlap between what's already been paid and what MYOB picks up from that point.

If you work through the reconciliation and it's still not lining up, speak with an advisor who can look at your file directly rather than troubleshooting further here.

https://www.myob.com/au/support/myob-business/payroll/paying-payroll-liabilities?productview=Browser

Update on this: Thanks to those that provided feedback, we've corrected an anomaly with the status indicator. Where a pay run had $0 super owing (nothing to pay), the status was correctly, but unhelpfully, showing as Unpaid. That's now fixed.

To be clear, that's separate from cases where super was genuinely paid, just outside MYOB (direct to an SMSF, or via a different clearing house). Unpaid in that case reflects that MYOB has no record of the payment, not that it wasn't made. 

If you're still seeing Unpaid on a pay run where every employee was paid through MYOB's Pay Super, let us know via a private message - the pay run date and employee details and we'll look into it.

I had unpaid super from October as a payrun for 6emloyees was sitting as having zero balances, rather than all the information I entered into the payrun. I have made a late super payment and checked the Year To Date Verification Report with the payroll summary and payroll register report and the figures there are correct. Can I proceed with the STP EOFY Finalisation or is there something else I need to do first?  

Hi TreeOak23,

Sorry this is happening. Definitely isn’t the experience we want you to have. For updates, you can follow and join this Community Forum thread. You’re welcome to add your post there as well, so the team can keep track of everyone impacted and share updates from the product manager in one place.

Cheers,

Doreen

I have the same issue, some pay runs showing as zero pay runs but amounts are correct on the payrun reports and listed as accepted by ATO after STP reporting.  

Liz

I posted this elsewhere two days ago and have been asked by Princess to add it to this thread, to keep it all in one place.

Paid super showing as unpaid

We implemented PayDay Super in October 2025 via MYOB AccountRight. For the July to September 2025 quarter, we had lodged and paid it via the ATO Small Business Superannuation Clearing House as normal (and have documented proof).

In preparing the STP Finalisation, it appears that the September quarter superannuation liability is erroneously marked as Unpaid in the Superannuation payments report.

I've come here to the community page to ask for advice, however I can see that others have had similar issues with paid super showing as unpaid over the past few years.

This is ridiculous! Has anything been done by MYOB to fix this? How are we supposed to maintain accurate payroll records?

I have the same problem, all my super is showing as paid in the super payments page & in the payrun itself, but in the payruns page it all shows as unpaid. When will this be fixed?

Simon-C​ I  think everyone on this thread knows the difference so don't insult us by telling us to check something all of us have already checked before. 

Still not working. 

Kolandasimone​ you have nothing to worry about then. Use the Super Payments screen status to guide you.

We will see what is causing some people to see a stale status in the Pay Runs screen. I understand that this is a concern you don't need. You have done the right thing.