EOFY Payroll Checklist 2026: What Australian Businesses Need to Get Right

Written By Carlie Clark

End of financial year (EOFY) is one of the most critical times for payroll.

It’s not just about closing the books, it’s about ensuring compliance, accuracy, and readiness for the new financial year.

To help you stay on track, here’s a practical checklist of what Australian businesses should be reviewing before 30 June 2026.

1. Review and Reconcile Payroll Data (Before 30 June)

Start by ensuring your payroll data is complete and accurate.

This includes reviewing:

  • All pay runs for the year, including earnings, allowances, overtime, deductions, and leave

  • PAYG withholding totals against your BAS lodgements

  • Superannuation accruals, ensuring the correct 12% super guarantee rate has been applied

Catching discrepancies early will save time, and reduce the risk of compliance issues later.

2. Check Your Superannuation Obligations

Superannuation is a key focus at EOFY, and timing matters.

Make sure you:

  • Confirm super for Q1–Q3 has been received by funds before 30 June to claim deductions

  • Plan for Q4 contributions, which are deductible if received by 28 July 2026

  • Identify and correct any shortfalls before 30 June to avoid the Super Guarantee Charge

It’s also important to start preparing for Payday Super, which will change how super is processed from 1 July 2026.

3. Complete Your STP Finalisation

Single Touch Payroll (STP) finalisation is a critical EOFY step.

Key actions:

  • Finalise STP by 14 July 2026

  • Mark all employee income statements as “Final”

  • Verify that wages, tax withheld, allowances, bonuses, salary sacrifice, and super are correct

Accurate STP reporting ensures employees can complete their tax returns without issues.

4. Review Payroll Compliance Requirements

EOFY is the perfect time to confirm your broader compliance obligations are met.

This includes:

  • Meeting all PAYG withholding requirements

  • Reviewing whether Fringe Benefits Tax (FBT) applies

  • Lodging your annual payroll tax return (if applicable)

Staying compliant helps avoid penalties and keeps your business aligned with regulatory expectations.

5. Update Awards and Employment Conditions

Changes to awards and wage rates often take effect from 1 July.

Before the new financial year:

  • Check for updates via the Fair Work Ombudsman

  • Update your payroll system to reflect any wage increases or changes

Ensuring your system is up to date will help you avoid underpayments or compliance risks.

6. Maintain Accurate Records and Reporting

Strong record-keeping is essential, not just at EOFY, but year-round.

Make sure you:

  • Retain payroll records for at least five years

  • Back up payslips, payroll reports, and superannuation records

Clear documentation supports compliance and makes audits or reviews much easier to manage.

7. Take the Opportunity to Review and Improve

EOFY isn’t just about compliance, it’s also a chance to optimise your payroll processes.

Consider:

  • Reviewing leave balances and liabilities

  • Auditing payroll access and permissions

  • Checking salary packaging arrangements

These steps can help improve efficiency, reduce risk, and set your business up for a smoother year ahead.

How PaysOnline Can Help

At PaysOnline, we support businesses through EOFY and beyond, ensuring payroll is accurate, compliant, and efficient.

From day-to-day processing to legislative updates, our team helps reduce admin pressure so you can focus on running your business.

 

Carlie Clark
Next

Payday Super: What This Shift Means for Your Payroll Process and How to Prepare