Scope note. This brief covers the super guarantee as it sits inside payroll processing and BAS Agent services - calculation, payment timing, reporting and the Super Guarantee Charge. It is an educational guide, not personal advice. For questions about deductibility or your income tax position, speak to your registered Tax Agent.
Payday Super switched on for wages paid from 1 July 2026. Three pay cycles in, the pattern of what goes wrong is already clear - and it is almost never the super calculation itself. It is the timing, the plumbing between payroll and the fund, and a handful of assumptions carried over from the quarterly regime that no longer hold. This is what the first 90 days have looked like inside the businesses we run payroll for, and what fixes each problem.
1. The 7-business-day clock starts on payday, not when you remember
Under the old rules you had until the 28th of the month after each quarter. Now, for every pay run, the contribution must be received by the employee’s fund within seven business days of the day you paid the wages (the ATO calls this the “qualifying earnings day”). Two words matter there. Received: the day you press pay in your clearing house is not the day the fund gets the money.Business days: weekends and national public holidays do not count, but the clock does not pause because your bookkeeper is on leave.
The practical consequence is that super has moved from a quarterly back-office task to a step inside every pay run. If you pay fortnightly, you now have 26 super deadlines a year, not four. The businesses coping best have simply made “submit super” the last click of the pay run, the same day, every time.
2. The clearing-house gap caught the smallest employers
The ATO’s free Small Business Superannuation Clearing House closed on 30 June 2026. Employers who had used it for a decade found themselves choosing a commercial clearing house or their payroll software’s built-in super service in the same fortnight they were trying to finalise STP for the old year. Some made the switch late; a few made their first July pay run with no clearing house connected at all.
The fix is mechanical but it has to be done properly: register with the new clearing house, confirm every employee’s fund details and member numbers have migrated, and run a small test contribution before the first real pay run. Each clearing house has its own processing time - typically one to three business days - and that time comes out of your seven. Know your provider’s cut-off and build the pay-run calendar around it.
3. Qualifying Earnings is broader than OTE - and payroll software did not always know
Super is now calculated on Qualifying Earnings (QE), which includes salary-sacrificed super and some amounts that fell outside Ordinary Time Earnings. For most employees the figures are identical. For anyone salary-sacrificing, or on an arrangement with unusual allowances, the 12% is now worked out on a larger base. We have seen payroll files where the QE setting had not been enabled, so July contributions were calculated on the old OTE basis and came in short - a shortfall the ATO can see directly from your STP reporting.
Check the super calculation basis in your payroll settings, then spot-check one salary-sacrifice employee by hand: 12% of their QE should equal what was sent to the fund.
4. What the ATO is actually doing about late super in year one
The ATO published a practical compliance guideline (PCG 2026/1) setting out how it will treat employers in the transition year. In plain terms:
- Lower risk: you attempted to pay super for every payday, on time and in full; a contribution was rejected, delayed or left unallocated by the fund; and you fixed it as soon as you knew. The ATO is not prioritising these employers for review.
- Medium risk: you kept paying quarterly as if nothing had changed. The contributions arrive, but they are late for most of the pay runs in the quarter.
- High risk: super is still unpaid after the old quarterly due dates, or you have not attempted to pay for each payday at all.
A rejected payment that you correct and resubmit inside the seven business daysstill counts as on time. A rejection you ignore until it falls outside the window becomes a late payment.
5. Late is now expensive, automatic, and allocated for you
Miss the window and the Super Guarantee Charge applies: the shortfall, notional earnings to compensate the employee, and an administrative uplift that can reach 60% of the shortfall. Two things changed with Payday Super. First, you no longer lodge an SG statement - the ATO identifies the shortfall from your STP and fund data and issues the assessment itself. Second, a late contribution is allocated automatically to the earliestoutstanding shortfall, not to the pay cycle you intended. Miss two fortnights and then pay on time for the third, and that payment is applied to the first miss; you are still behind.
If you know you have missed a pay run, a voluntary disclosure to the ATO before an assessment issues reduces the administrative uplift - and the earlier the disclosure, the larger the reduction. The SGC remains non-deductible, which is why avoiding it matters more than any fee you will pay to get payroll right.
6. The 90-day checklist
- Super submitted as the last step of every pay run, the same day, by one named person.
- Clearing-house cut-off time known and written into the pay-run calendar.
- QE basis confirmed in payroll settings; one salary-sacrifice employee checked by hand.
- Super rate confirmed at 12% for every employee record, including new starters.
- Fund rejections monitored daily in the clearing house, not discovered at month-end.
- Weekly reconciliation: STP-reported super for the period equals contributions received by funds.
- A written process for a missed payment: pay immediately, then disclose to the ATO.
The quarterly super habit was 30 years old; it is not surprising it has taken a few pay cycles to unlearn. If you want to see what the per-payday timing does to your working capital, the Payday Super impact calculator models it against your own payroll. If you would rather the whole process ran without you thinking about it, that is what our payroll service is for.
References: ATO - Paying super on payday, payment deadlines for Payday Super, and Practical Compliance Guideline PCG 2026/1; Treasury - Payday Super legislation (effective 1 July 2026); ATO - Super Guarantee Charge. Figures and rules current at 17 July 2026.
This information is general in nature and does not constitute personal financial or tax advice. Please contact us to discuss your individual circumstances. Tax laws are subject to change; information on this page reflects legislation in effect as of July 2026.