Payday Super: A Bookkeeping Checklist for Australian Employers

Since 1 July 2026, Australian employers pay superannuation guarantee with each payday instead of quarterly. The first full quarter under Payday Super has just ended, and for many businesses it exposed the same gaps: super clearing late, payroll liability accounts that never reach zero, and STP figures that do not match what was paid.

This checklist is for owners and bookkeepers who run payroll in Xero, MYOB, QuickBooks or Employment Hero. It covers the bookkeeping side. For the rules themselves, including the exact timeframes and exceptions, check the ATO's Payday Super guidance or ask your registered agent.

What actually changed

• Super is due on each payday's qualifying earnings, not by the 28th day after quarter end
• Contributions must reach the employee's fund within a short window after payday, so processing time at clearing houses now matters
• The ATO's Small Business Superannuation Clearing House has closed, so small employers need another way to pay
• The super guarantee charge applies when contributions are late or short, and is assessed much closer to the payday than before

Before the next pay run: setup checks

• Confirm your payroll software pays super through an integrated super solution or a clearing house that supports Payday Super
• Check every employee has valid fund details: USI, member number, or a stapled fund looked up for new starters
• Review pay items so ordinary time earnings are flagged correctly; overtime and some allowances are treated differently
• Make sure the super payment comes from an account with enough cash on payday, not a week later
• Set up a separate super liability account if wages and super currently share one

Every payday: a short checklist

• Pay run approved and STP pay event submitted
• Super calculated on the right earnings for every employee, including casuals and new starters
• Super payment authorised the same day as wages, or as close as your process allows
• Payment confirmation saved from the clearing house or payroll software
• Any rejected contributions (wrong fund details, closed accounts) fixed and resent straight away

Every week or month: reconcile

The quickest test of whether Payday Super is working is your super liability account. After each pay cycle it should return to zero once contributions clear. A growing balance means something was calculated but not paid, or paid but not matched.

• Super liability account reconciled to nil after each pay cycle
• Bank lines for super payments matched to the payroll liability, not coded to expenses
• Rejected or refunded contributions tracked until resolved
• Year-to-date super in STP compared with the ledger each month, not only at 30 June

At BAS time

Super itself is not reported on the BAS, but the same pay runs drive W1 (total salary and wages) and W2 (PAYG withheld). If super is out of balance, the payroll setup often has other problems too. Reconciling wages, PAYG withholding and super together before each BAS catches errors while they are still easy to fix.

Common problems we see

• Super still paid quarterly out of habit, with the liability building for weeks
• Clearing house payments made on payday but taking several business days to reach funds
• Super payments coded to super expense, doubling the cost in the profit and loss
• New starters with no fund details, so contributions bounce
• Back pay or termination payments processed outside the normal pay run and missed for super

Where outsourced bookkeeping helps

Payday Super turns a quarterly task into a per-pay-run task, and that is where small businesses fall behind. A bookkeeper can prepare each pay run, reconcile super after every cycle, and flag rejected contributions before they become late. Approval, payment and the STP submission stay with you.

If your business is behind after the first quarter, start by reconciling the super liability back to July. It shows exactly which paydays need attention.