The end of financial year can sneak up on even the most organised small business owner, especially when payroll is in the mix. Between finalising pays, reporting to the ATO, and staying compliant with changing rules (hello minimum wage increases!), it’s easy to miss a step.

Here’s a practical EOFY payroll checklist tailored for small business owners with the essentials you actually need to tick off.

7 payroll checks for EOFY

1. Check you’re using the right modern award and rates

Wage increases kick in from 1 July, but now’s the time to double-check you’ve applied the right award classification and current minimum pay rates before your final June pay run. Fair Work’s Pay Calculator is your best friend here.

Tip: If you’ve got casuals or part-timers, check whether they qualify for loading, overtime or penalty rates – underpayment headaches are the last thing you need right now.

2. Finalise Single Touch Payroll (STP) reporting

Under STP Phase 2, your final EOFY pay event must be lodged with the ATO no later than 14 July 2025. That means:

All year-to-date figures are accurate and reconciled.

All terminated employees are included.

Fringe benefits (if applicable) are correctly reported.

Reminder: You don’t need to provide traditional payment summaries anymore – employees will access their income statement through myGov.

3. Reconcile your superannuation contributions

Super contributions must be paid before 30 June to be tax deductible this year. Check that:

Super has been calculated correctly on ordinary time earnings (OTE).

You’ve used the right clearing house or payment method.

Payments allow 5+ days for processing before EOFY.

Heads up: The Super Guarantee rate increases to 11.5% from 1 July 2025, so update your payroll software settings in advance.

4. Audit employee leave balances and entitlements

This is the perfect time to:

Review accrued leave (especially for long-service leave thresholds).

Check that leave has been correctly accrued and recorded.

Clarify any carry-over rules in awards or agreements.

Try this: Encourage staff with big leave balances to plan some time off – it’s a win for wellbeing and your balance sheet.

5. Prepare any bonuses or EOFY commissions

If you’re rewarding your team for a big year, make sure bonuses are:

Processed through payroll and taxed correctly.

Included in STP reporting.

Allocated in the correct financial year (if paid in July but accrued in June).

Tip: You can delay the payment but still accrue it for EOFY tax purposes – just chat with your accountant.

6. Keep your records clean and ATO-ready

Now’s the time to tidy up those loose ends.:

Update employee contact and TFN details.

Double-check ABN and bank account info.

Ensure your payroll records meet the ATO’s 5-year record keeping requirement

Tip: Store everything securely and in one place – whether cloud-based or on your accountant’s books.

7. Don’t forget: Tax time is also planning time

Once your EOFY payroll tasks are done, use the new financial year to review systems, consider automation (hello AI payroll tools!), and speak with your bookkeeper or accountant about upcoming changes – like the STP penalty amnesty ending and Superannuation Guarantee charge changes.

Want more EOFY advice?Ccheck out our finance hub

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