Every year, 30 June catches founders off guard. You’ve been heads-down on product, hiring and customers, and then suddenly it’s mid-June and your accountant is chasing you for records you haven’t thought about since July last year.
EOFY isn’t complicated if you stay on top of it. But leave things too late and you’re looking at missed deductions, ATO penalties and a very stressful few weeks. Here’s what to work through before the financial year closes.
Get your superannuation contributions in on time
Super is one of the biggest EOFY traps for startup founders. To claim a tax deduction for super contributions in the 2025-26 financial year, the payment must be received by your super fund before 30 June – not just sent.
For employee super, that means processing well ahead of the cut-off. Banks can take a few days to clear, and super funds have their own processing timelines. If you’re tight, aim to have contributions out by mid-June at the latest. Late super also attracts the Superannuation Guarantee Charge, which is not deductible and comes with penalties on top.
If you’re a founder paying yourself a salary, don’t forget your own super either. A concessional contribution to your personal super fund before 30 June is deductible and often overlooked.
Finalise your payroll through Single Touch Payroll
If you have employees, you’re required to submit your STP finalisation by 14 July. But getting this right means having clean payroll records before EOFY, not scrambling after it. Check that all pay runs are reconciled, that termination payments are correctly coded and that any salary sacrificed amounts are accurately reported.
Your employees can’t lodge their personal tax returns until you’ve finalised your STP data, so it’s worth treating this as a June task rather than a July one.
Check your BAS position and outstanding lodgements
Heading into EOFY with overdue BAS lodgements is a problem you don’t want. The ATO is more likely to flag accounts with outstanding obligations for review, and penalties compound quickly. If you’re behind, lodge and pay what you can before 30 June.
Also worth reviewing: your GST registration status. If your turnover has crossed $75,000 this financial year and you haven’t registered for GST, that’s an urgent conversation to have with your accountant.
Prepay deductible expenses before 30 June
Prepaying certain expenses before 30 June can bring forward deductions into the current financial year. This includes things like insurance premiums, subscriptions, rent and interest on business loans – as long as the prepayment period doesn’t extend more than 12 months beyond the date of payment.
This is a legitimate and widely used strategy. If your business has cash available and predictable upcoming expenses, it’s worth discussing with your accountant whether prepaying makes sense for your position.
Write off bad debts and obsolete assets
If you have invoices from customers you know you’re never going to collect, write them off as bad debts before 30 June. The debt needs to be genuinely bad – not just slow-paying – and you should have documented your attempts to recover it.
Similarly, if you have assets that are no longer in use or worthless, write them off the books. The instant asset write-off provisions may also allow you to immediately deduct the full cost of eligible depreciating assets purchased and used during the year – check with your accountant on current thresholds, as these change.
Register your R&D activities if you haven’t already
If your startup has been conducting eligible R&D activities this financial year, you need to register with AusIndustry within 10 months of the end of your income year – so by 30 April 2027 for the 2025-26 year. But the sooner you start pulling your records together, the better.
Documentation is everything with R&D claims. If you haven’t been keeping records of your eligible activities throughout the year, use the lead-up to EOFY to reconstruct what you can while it’s still fresh.
Get your books in order now, not in July
The single best thing you can do before 30 June is hand your accountant clean, reconciled books. That means bank feeds reconciled, expenses categorised, invoices matched and any director loan accounts documented and understood.
The earlier your accountant can close off the year, the earlier you’ll know your tax position – and the more time you have to make decisions before the deadline hits.
Ready for EOFY but not sure where to start?
At Standard Ledger, we work with Australian startups year-round to keep their books clean and their compliance on track – so EOFY doesn’t become a crisis. If you want to head into 30 June with your house in order, get in touch and let’s talk through what needs to happen.
