Your EOFY payroll checklist for 2025-26

End of financial year has a way of arriving faster than anyone expects. The good news is that a smooth finalisation is mostly about preparation. If your employee data is clean, your pay runs are reconciled and your categories are set up correctly, lodging your finalisation becomes a quick confirmation rather than a scramble.

This is our recommended checklist to work through before you finalise and lodge for the 2025-26 year. It is a broad guide rather than step by step instructions for any one payroll system, and what applies to you will depend on your setup. Use it as a starting point, and talk to us about anything specific to your organisation.

Three key dates to keep in mind

Before the checklist, it helps to have the key dates clear:

30 June 2026. This is the last date a pay run's payment date can fall on to count in the 2025-26 financial year. It is the payment date that matters, not the period the work was done in.

1 July 2026. New modern award rates apply from the first full pay period starting on or after this date. EOFY and the annual wage increase land in the same window, so it is worth planning for both at once.

14 July 2026. This is the ATO due date to lodge your Single Touch Payroll finalisation for most employers. Once you lodge, your employees' income statements show as tax ready in their myGov account. Longer deadlines can exist in some circumstances where you engage Closely Held Payees or are granted an extension by the ATO, so seek additional support for your organisation's obligations.

The EOFY payroll checklist

1. Review and update employee details

Start with your data. Check that tax file numbers, email addresses, postal addresses and super fund details are current and complete. This is easy to overlook and surprisingly common to get wrong, especially for employees who have moved or changed contact details during the year. Clean records mean income statements reach the right people and your finalisation does not get held up by validation errors.

2. Verify which financial year each pay run belongs to

A pay run belongs to the financial year of its payment date, not the period the work was performed in. Every pay run with a payment date on or before 30 June 2026 sits in 2025-26, and anything paid from 1 July onwards falls into the new year. Map out your pay calendar around this so a late June or early July run does not accidentally land in the wrong year. If you are unsure how a particular run will be treated, it is worth confirming before you finalise.

3. Reconcile and finalise your pay runs

Make sure every pay run with a payment date up to 30 June has been completed and finalised. Then reconcile your year to date figures, gross wages, tax withheld, superannuation and allowances, against your own records. Reconciling before you lodge is what catches issues while they are still easy to fix. Investigate any variances rather than assuming the system has it right.

4. Check your pay and deduction categories

Confirm that each pay category and deduction category is classified correctly. This includes which allowances are reportable and how they are reported, and whether deductions are treated as pre tax or post tax. Classification errors do not always show up during the year, but they flow straight through to employee income statements at finalisation, so this is a good time to review them carefully.

5. Audit salary sacrifice and reportable amounts

Review any salary sacrifice arrangements to confirm the amounts are correct and have been treated properly across the year. While you are there, check reportable employer super contributions and any reportable fringe benefits amounts that need to be included. If your organisation treats certain benefits as exempt, confirm that the exemption still applies, as it is easy for an arrangement to change without the payroll setup being updated to match.

6. Reconcile, then lodge your finalisation

Once your data is reconciled and any validation issues are sorted, lodge your Single Touch Payroll finalisation for the year. This is the step that tells the ATO your payroll data for 2025-26 is complete and marks your employees' income statements as tax ready. Aim to have this done on or before 14 July. If you need to add reportable fringe benefits amounts or foreign tax paid, make sure those are entered before you lodge.

7. Get set for the new financial year

EOFY is also the moment to look forward. New award rates apply from the first full pay period on or after 1 July, so check your payroll is configured to apply them correctly. It is also a sensible time to review pay rates against the award, confirm employment contracts reflect current obligations, and tidy up leave balances and entitlements before the new year gets underway.

How Effective HR can help

EOFY touches data, payroll, award interpretation and compliance all at once, and the right approach genuinely depends on your organisation. Whether you want a hand with one item on this list, the whole thing, or just a second set of eyes before you lodge, our team can help.

Book a meeting with us and we will walk through what end of financial year looks like for your organisation. You can also call us on 1300 28 28 16, or reach the team at contact@effectivehr.com.au.

*This article is general information only and does not take your specific circumstances into account. For advice tailored to your organisation, please get in touch with Effective HR.*