EOFY Checklist 2026: A Perth Small Business Guide to the Last Six Weeks

What needs to be lodged, paid and reconciled before 30 June, plus what is changing the day after.

The end of financial year always carries the same recurring obligations, but EOFY 2026 sits at the cusp of the largest superannuation reform in three decades. Every Perth small business that pays wages will move from quarterly super to Payday Super from 1 July, which means the work you do in May and June, the final quarterly BAS, STP finalisation, the last quarterly super payment, and end of payroll year reconciliation, all carry forward into a new operating system on 1 July. Get the EOFY checklist right this year and the first quarter of 2026 to 2027 runs smoothly. Get it wrong and the new payday cycle compounds the problem within weeks.

Below is the run sheet we work through with every Perth small business client between now and the end of July. It assumes you have been bookkeeping along the way. If you have not, the priority order is the same, you just need to compress the timeline.

Your final quarterly BAS for the April to June quarter

The Q4 2025 to 2026 BAS covers GST, PAYG withholding, and PAYG instalments for the April to June period. Self lodgement is due 28 July 2026, with paper lodgement also closing on the same date. Businesses using a registered BAS agent benefit from the BAS and IAS lodgement program extension, which typically runs to 25 August 2026.

For most Perth small businesses the practical risk is not the lodgement date itself but the lead up reconciliation. GST collected and paid needs to match what is in your accounting software. PAYG withholding needs to reconcile to STP. PAYG instalments need to be reviewed against your year to date taxable position. If your instalments are running well above your actual income, your last opportunity to vary them down for the current year is the Q4 BAS itself, a variation that a BAS agent can lodge on your behalf.

We see a recurring pattern where Perth businesses lodge Q4 BAS at the deadline, then receive a refund or shortfall surprise three weeks later because the reconciliation was rushed. The fix is to reconcile the general ledger by mid June, not late July.

STP finalisation by 14 July 2026

Single Touch Payroll finalisation is the formal declaration that all gross wages, PAYG withholding, allowances, deductions, and reportable employer super contributions for the 2025 to 2026 financial year are accurate. Once finalised, the data flows to the ATO and pre fills your employees’ tax returns. The deadline for standard employers is 14 July 2026. Closely held employees, typically family members in a private company, have until 30 September 2026. Our payroll and STP services cover the full finalisation process for both employee categories.

Before you submit the finalisation declaration, three reconciliation steps need to be done. Payroll wages must reconcile to your profit and loss wages account. PAYG withholding totals must match what has been paid to the ATO across the year. And any reportable fringe benefits and employer super contributions need to be reviewed for completeness.

Errors at finalisation generate amendment requests during tax season, awkward employee conversations, and in some cases reissued payment summaries. Reconciling once, before the declaration, removes all of that.

Q4 super guarantee, the last quarterly payment

The June quarter super guarantee payment, covering 1 April to 30 June 2026, is due to your employees’ funds by 28 July 2026. This is the final quarterly super payment under the existing system. From 1 July 2026, the Payday Super rules apply.

Two things matter this quarter. First, the 12 percent SG rate still applies for the June quarter. The rate reached 12 percent on 1 July 2025 and stays at 12 percent under current law, despite some misinformation suggesting an increase to 12.5 percent. Second, the timing change from 1 July means any unpaid super sitting at the end of the quarter falls into a transition window the ATO is monitoring closely.

Payday Super requires employers to pay super contributions within seven business days of each payday from 1 July 2026. Quarterly payment ends. The super guarantee charge framework changes with it, every late or missed payment triggers an assessment per pay run, not per quarter. The compounding effect of late super becomes faster and more expensive.

Confirm your payroll software is on a Payday Super ready version before 1 July. Test a payday super run in June if your software supports a dry run. If your clearing house is not Payday Super compliant, move to one that is.

End of payroll year reconciliation

Beyond STP finalisation, end of payroll year is the right time to clean up the payroll register, confirm leave balances, reconcile workers’ compensation wages, and prepare your annual WorkCover WA wages declaration (due in the weeks following 30 June for most WA employers). This is part of our standard year end reconciliation work for retainer clients.

For Perth businesses with award covered staff, this is also the cycle where award rate updates from 1 July need to be loaded into your payroll software. The Fair Work Commission’s annual wage decision is typically released in early June and takes effect from the first full pay period on or after 1 July. The end of June is also the cleanest cut off for finalising any salary sacrifice arrangements that should be reset for the new financial year.

The clients we see breeze through July are the ones that closed payroll cleanly in late June. The ones still chasing reconciliations in mid August are the ones that left payroll year end until after the Q4 BAS was lodged.

What to give your accountant for the income tax return

Once BAS is lodged and STP is finalised, the next handover is to your accountant for the income tax return. The handover is faster, cheaper, and more accurate when the bookkeeping side is reconciled first. The essentials we prepare for clients as part of our Xero bookkeeping service include a clean trial balance with bank, GST control, PAYG control, and wages all reconciled, a fixed asset register updated with new purchases, loan statements reconciled to balance sheet, year end stocktake completed for businesses holding inventory, and director loan accounts cleaned up before year end.

The 20,000 dollar instant asset write off is being made permanent for businesses with turnover up to 10 million dollars from 1 July 2026, but the threshold remains the same for assets purchased before 30 June. Division 7A on director loan accounts remains one of the most common surprises for small company owners at tax time, and is best dealt with before 30 June rather than discovered in October.

The earlier this package is with your accountant, the more time they have to identify legitimate deductions before the return is lodged. Late June is busy. Late July is busier. The work itself does not change, but the queue does.

Speak to a Perth bookkeeper before 30 June

If you need a hand getting your BAS reconciled, STP finalised, payroll closed, and the handover package ready for your accountant, the next six weeks are when the work is done.

My Bookkeeper Perth has been working with Perth small businesses for over nineteen years. Justine Jarratt is a TPB registered BAS agent based in Southern River, working with trades, hospitality, professional services, and family run businesses across the Perth metro area. We handle BAS and IAS lodgement, payroll and STP, super compliance, and the year end reconciliations that make your tax return smoother. Call (08) 9490 9555 or book a free, confidential consultation through our contact page.