Published: July 2025
The EOFY payroll checklist is an essential tool for navigating this busy time of year, with multiple deadlines to meet and reporting requirements to follow. It’s not just about processing the final pay run—there’s a lot more involved.
Whether you're an experienced payroll professional or tackling it for the first time, our expert trainers have created this step-by-step checklist to help you navigate the process confidently and ensure nothing important slips through the cracks.
Table of Contents
9 Steps to Run EOFY Payroll
- Information Housekeeping – As part of your EOFY payroll checklist, it's essential to verify that all employee data is accurate and up to date. This includes checking Tax File Numbers (TFNs), dates of birth, and any termination dates for former employees, unused pay items, and fringe benefits amounts if you have any. Ensuring this information is correct helps prevent reporting errors and delays with the ATO.
- Reconcile Payroll – Once all pay runs for the financial year have been processed, it’s time to reconcile your payroll. This involves comparing reports, such as the Payroll Register and Payroll Activity, to ensure they match, and reviewing your STP year-to-date (YTD) totals against payroll summaries. Any discrepancies should be identified and corrected before finalising. Accurate reconciliation ensures your EOFY reporting is complete and compliant.
- Superannuation – Check that all superannuation contributions for the year have been calculated correctly and reconciled. Compare your profit and loss report (super expense) with your balance sheet (super payable) to confirm totals align. If you want to claim a tax deduction for super, make sure contributions are paid and received by the fund before 30 June.
- Reconcile PAYGW – Review your Pay As You Go Withholding (PAYGW) totals by reconciling your Payroll Summary against your balance sheet. This ensures the amount withheld from employee wages matches what’s reported on your BAS or IAS. Keeping PAYG records accurate helps avoid errors and penalties.
- Other deductions – Reconcile any additional employee deductions made throughout the year, such as salary sacrifice amounts, union fees, child support payments, or other withholdings. Use your payroll category and balance sheet reports to verify all deductions are correctly recorded and up to date.
- Complete STP Finalisation – You’re now ready to complete your STP finalisation with the ATO. This step must be done by 14 July each year. Review all figures one last time and make sure any Reportable Fringe Benefit Amounts (RFBAs) are entered if required. Once submitted, employees will be able to access their income statements via myGov.
- Print or email your payment summaries – While payment summaries can be provided electronically, it's still important to let your employees know how to access them. Clear communication ensures they can retrieve their records without confusion or delay.
- Make a backup and store it in a safe place – Before rolling into the new financial year, create a complete backup of your payroll data. Save it securely and ensure it’s accessible if needed for audits, amendments, or record-keeping purposes. This is a key part of your EOFY housekeeping.
- Post Finalisation – After finalisation, update your payroll settings for the new financial year. This includes increasing the Super Guarantee (SG) rate to 12% from 1 July 2025, reviewing any applicable wage increases, and confirming tax tables are up to date. Once done, you’re ready to start fresh for the new year.
Finalising your payroll every EOFY is more than just a routine task; it’s also about staying compliant and making sure your employees are paid correctly.
Upskill with Applied Education
At Applied Education, we offer nationally recognised qualifications including the Diploma of Payroll Services and the BAS Agent Registration Skill Set. Whether you're aiming to deepen your payroll expertise or meet TPB registration requirements, our courses are designed to give you the knowledge and confidence you need.
We’ll also be updating our Payroll Updates and Salary Packaging courses online to help you stay up to date with the latest compliance changes.
For further details on these courses, please visit our Payroll Updates and Salary Packaging pages.
