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

LucyMik

Hi All

We paid on time all our super through MYOB Hub But when is see the payrun page the super seems unpaid for several months not just the last pay.

When i go to super payments looks fine completed, why is this discrepancy?

I hope this will not causing any problem at the end of month/financial year.

I have also tried the reset button in payrauns but same result.

See the attachments

Super payments complited.pdf

Payrun show unpaid Super.pdf

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Simon-C

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:

Reconcile your super liability account in MYOB to confirm which periods were paid via SBSCH and which, if any, are genuinely outstanding.
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.
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

Simon-C

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.

Heidi789

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?

SharonSL

My super payments all show as paid but I still have a few random ones from earlier periods saying Unpaid in the Pay Runs screen.

Princess_R

Hi @TC1808,

Thanks for following up. I checked with the team, and they confirmed that an update was rolled out yesterday as Payday Super came into effect. Super payments should now be showing as paid.

Cheers,

Princess

MichaelaJohnson

Same issue. MYOB please provide an update.

TC1808

I am also having this exact same problem dating back into 2024. Have definitely paid all super contributions. Would appreciate a solution.

HelloHelen

Hi - we also have 6 super payments randomly showing as unpaid that have definitely gone through dating back to April this year, totally agree this is very confusing. I have been paying our super weekly so everything is balanced for EOFY as far as I am aware, just doesn't look like it on this page ??

Regards

Helen

AMZConstruct

Hi,

I have the same issue with one my super payments.

Regards,

AMZ

Genreve_S

Hi everyone,

Thanks for sharing this, it certainly is something the dev team has been looking into. If your Super Payments page shows the payments as Completed, but the Pay runs page is still showing those amounts as unpaid, it would be best to lodge a support case through My Account so the team can investigate this further.

If you do, please include your serial number. A screenshot of the Pay runs page showing the unpaid super would also be quite helpful.

That will help the team review the issue more closely in a secure setting, and get you to receive updates regarding your cases.

Rergards,
Genreve

MThurston

I have this problem also . I emailed myob 2 weeks ago and have not heard a thing back . Very annoying

Kolandasimone

My file is the same. Under pay runs it shows 90% of the Super as unpaid although it is clearly paid. I pay weekly at the same time I do payroll.

Marquette94

I’m seeing a few people mention the same thing, so I don’t think it’s anything you’ve done wrong. So if Super Payments shows Completed, that’s probably the place I’d trust more for now. Not sure it will cause any month-end or EOFY issue, but hey, I’d still keep screenshots or export the Super Payments report just in case.

Gregwa

Good morning, Happy Kings Birthday, I have the same problems as all of the above. Some unpaid, although all super payments have been paid..

Thank you

Greg

Fabs01

Hi @Princess_R

We are also having the same issue the Pay Run are not syncing with the Super Payments page. I have started pay day super already and all showing up unpaid under Pay Run.

Regards

Rebecca

Khosk

Princess we also have similarly affected Super payments. Can you please mark our file as affected also?

Thank you.

LucyMik

I have paid all super through MYOB , nothing unpaid at the super payments all are clear paid. the Pay runs looks unpaid some from Nov25 for 2 of my clients.

What you mean to clear this amounts via GJ? I dont get it

SharonSL

I have just noticed that my file is affected also - on the 'Pay Runs' page super payments are showing as In Progress or Unpaid but they have been paid - I pay super monthly. However after paying the super for today's payrun (Payday Super for the first time) the 'Super Payments' page shows all previous super payments as Completed.

dieseldigit

@LucyMik if you have unpaid super that relates to prior periods before the Pay Super came to light for us all, then you will need to clear these amounts out via a GJ

Earl_HD

Hi @aimfit,

Thanks for raising this, I've also marked your file as affected. If there’s an update, you’ll receive an email from us with the next steps, including anything you may need to do in your file.

Regards,
Earl

LucyMik

I have also checked every fund if its ticked the Pay directly from AccountsRight, was all ok.

So not here the problem

aimfit

I also have the same problem. Out of all April super payments I still have one marked as 'unpaid' (even though it is paid), and all other reports say it is completed.

Regards,

Aimee

Earl_HD

Hi @Piin-Nan,

Thanks for sharing those extra details. Our team is fully aware of this issue, and we’ve marked your file as affected. There’s nothing further you need to do at this stage.

If there’s an update, you’ll receive an email from us with the next steps, including anything you may need to do in your file.

Regards,
Earl

Piin-Nan

Hi Princess,

I also have the same issue as mentioned above but just one payment out of the four that we have made is showing the discrepancy. We only started using MYOB super payment in April. In the "Pay Run" it states "Unpaid" but in the "Superannuation Payment" Report the amount is shown as "Paid". The rest of the super payments matched in the reports.

It would be most appreciated if you could also let me know what needs to be done after you have an update from MYOB.

Many thanks

Piin-Nan

Princess_R

Hi @LucyMik,

Appreciate you raising this with us. It’s definitely a bit odd to see the Pay Super status and the Pay Runs super status not lining up properly, as those should normally match.

I’ve reached out to the team and passed your post on, and they’ve now identified it as a sync issue between those two areas. A ticket has been raised on their side and is being treated as a priority. I’ll come back to you with an update as soon as I hear more from the team.

Cheers,

Princess