To prepare payroll for an audit before EOFY, verify every employee’s details (TFN declaration, super fund, tax status), reconcile each pay run against timesheets, rosters, bank payments and your STP-reported totals, confirm superannuation was calculated on all ordinary time earnings at 12% and paid to the correct funds on time, and check award classifications, penalty rates and minimum engagements were applied correctly all year. Then lock it in: finalise Single Touch Payroll by 14 July and keep every record for 7 years. Catching issues before 30 June is far cheaper than amending payment summaries and back-paying super after the year has closed.
End of financial year brings more than just tax returns — it’s when payroll accuracy matters most. Whether you’re facing an internal review, an external audit, or simply want clean books going into the new year, preparation is essential. The Australian Taxation Office and Fair Work Ombudsman both apply increased scrutiny to employer compliance, making proactive audit preparation a business necessity rather than optional housekeeping.
This guide is a practical checklist for getting your payroll systems audit-ready and EOFY-ready: which records to verify, the common problem areas, a structured reconciliation process, and the finalisation dates you can’t miss. Comprehensive payroll and compliance reporting makes each of these steps faster. For the full step-by-step finalisation process — including STP finalisation and super deadlines — see our guide on how to complete EOFY payroll. If you also want to sanity-check your final pay runs before they process, our companion piece on payroll validation before EOFY covers the pre-pay-run checks that stop errors reaching this stage.
Quick summary
- Start early:
Begin EOFY preparation 8-12 weeks before 30 June
- Verify details:
Confirm employee details, TFN declarations, and super fund information
- Reconcile everything:
Match pay runs to timesheets, rosters, bank payments, and STP-reported totals
- Hit the dates:
Super to funds before 30 June, STP finalised by 14 July, records kept 7 years
Why EOFY payroll preparation matters
Proactive preparation before end of financial year delivers several benefits.
Avoid costly corrections
Errors discovered after EOFY require amended payment summaries, adjusted superannuation contributions, and potentially back-pay calculations that span financial years. These corrections are complex, time-consuming, and may trigger additional ATO scrutiny. Finding and fixing issues before 30 June is significantly easier and less expensive.
Ensure STP compliance
Single Touch Payroll requires accurate reporting of wages, tax, and superannuation to the ATO with each pay run. EOFY finalisation must reconcile all STP reports for the year. Discrepancies between your records and STP submissions need resolution before the finalisation deadline.
Protect against Fair Work audits
The Fair Work Ombudsman conducts targeted compliance campaigns and responds to employee complaints. Having organised, accurate records demonstrates due diligence and makes any audit process smoother. Employers who can quickly produce complete records face far less disruption than those scrambling to reconstruct history. For the formal process, see our guide on how to conduct a payroll audit.
Maintain employee trust
Employees notice when their income statements contain errors or when super contributions don’t match their records. Accurate EOFY processing demonstrates professional HR management and maintains the trust that keeps good staff engaged.
The EOFY preparation timeline
Effective preparation follows a structured timeline.
8-12 weeks before EOFY: initial review
Run year-to-date payroll reports and identify any obvious anomalies. Check for employees with unusual hours patterns, unexpected leave balances, or missing information. This initial scan reveals areas requiring deeper investigation.
6-8 weeks before: employee data verification
Contact employees to verify personal details, tax file declarations, and superannuation fund choices. Update any changes and ensure all mandatory information is current. This prevents issues with income statements and super contributions.
4-6 weeks before: reconciliation
Reconcile payroll records against timesheets, rosters, and bank statements. Verify superannuation contributions match payroll records. Check leave balances and accruals are calculating correctly. Investigate and resolve any variances found.
2-4 weeks before: award compliance check
Review pay rates against current award rates. Check that penalty rates have been applied correctly for all shifts. Verify casual loading, allowances, and minimum engagement requirements have been met throughout the year.
Final 2 weeks: corrections and finalisation
Process any required corrections before the final pay run of the financial year. Ensure all adjustments are documented. Prepare for STP finalisation and generate EOFY reports for accountant review.
Key areas to check before EOFY
Focus your audit preparation on these critical areas.
Employee information
Verify current addresses, TFN declarations, tax-free thresholds claimed, HELP/HECS debt declarations, and superannuation fund details. Missing or incorrect information affects income statements and tax reporting.
Pay rates and classifications
Check that all employees are on correct award classifications with current pay rates using award interpretation tools. Verify any pay increases were applied from the correct date. Confirm casual loading is applied consistently.
Hours and penalty rates
Reconcile timesheet hours against paid hours using your rostering software. Verify penalty rates were applied for evenings, weekends, and public holidays according to applicable awards. Check overtime calculations are correct.
Superannuation
Verify super has been calculated at the correct rate (12% for 2025-26) on all ordinary time earnings. Check contributions have been paid to correct funds within quarterly deadlines. Reconcile year-to-date super against payroll records.
Leave balances
Review annual leave, personal leave, and long service leave balances for accuracy. Check accrual rates are correct for each employee type. Verify any leave taken has been properly recorded and deducted.
Allowances and deductions
Check all allowances have been paid according to award requirements. Verify any salary sacrifice arrangements are correctly documented and processed. Ensure deductions are authorised and correctly applied.
Common payroll audit findings to check
Auditors frequently identify these issues — checking them proactively prevents problems.
Incorrect award classification
Employees classified at the wrong level for their actual duties. This affects base pay rates, overtime triggers, and penalty calculations. Review job descriptions against award definitions.
Penalty rate errors
Penalty rates applied from the wrong times or at incorrect percentages. Weekend and public holiday rates are frequently missed, and evening and night shift penalties are often calculated incorrectly.
Minimum engagement breaches
Casuals paid for less than the minimum engagement period required by their award. Three-hour minimums are common but vary by award and shift type. Short shifts are a frequent compliance gap.
Superannuation shortfalls
Super not calculated on all ordinary time earnings, contributions paid late incurring interest charges, salary sacrifice reducing super below minimum requirements, or wrong fund details causing failed payments.
The reconciliation process
Systematic reconciliation identifies discrepancies before they become audit findings. Work through each of these matches in turn.
Timesheet to payroll reconciliation
Compare total hours recorded in timesheets against hours paid in each pay run. Identify any variances and investigate the causes — manual adjustments, rounding, or errors. Integrated systems from time and attendance to payroll eliminate most manual reconciliation.
Payroll to bank reconciliation
Verify net pay amounts processed through payroll integration match bank payments. Check for any payments made outside the payroll system that need inclusion, and ensure refunds or corrections are properly recorded.
STP-reported to pay-run reconciliation
Match your year-to-date STP submissions against your finalised pay-run totals for gross wages, PAYG withholding, and super. This is the reconciliation the ATO relies on at finalisation — any gap between what you reported through the year and your actual pay runs must be resolved before you lodge, or employees’ income statements in myGov will be wrong.
Superannuation reconciliation
Match year-to-date super calculated in payroll against contributions actually paid to funds. Verify clearing house payments have reached nominated funds and check for any rejected contributions needing resubmission. From 1 July 2026, payday super changes for casual workers mean contributions must reach funds within 7 business days of each pay run — factor this into your process.
Leave balance reconciliation
Compare calculated leave entitlements against system balances. Check leave taken matches approved leave requests, and verify accrual rates are correct for employment type and length of service.
The EOFY finalisation dates you can't miss
Reconciliation gets your numbers right; these deadlines lock them in. Missing a finalisation or super date is one of the most common — and most avoidable — EOFY compliance failures, so mark them now.
Key 2025-26 EOFY payroll dates for Australian employers
| Date | What's due | Why it matters |
|---|---|---|
| By 30 June | Final pay runs processed and super contributions received by employee funds | Contributions must reach the fund (not just leave your account) by 30 June to be deductible in that year — allow ~2 weeks clearing time |
| 14 July | STP finalisation declaration lodged | Locks in employees' year-to-date data and releases their income statements in myGov |
| 28 July | Q4 super guarantee payment due | The final quarterly super deadline before payday super begins (1 July 2026) |
Dates reflect the standard EOFY cycle. Always confirm current deadlines with the ATO, as they can shift when they fall on a weekend or public holiday.
Don't forget terminated employees
Staff who left during the year still need to be finalised. Confirm their final pay was calculated correctly — including accrued annual leave, any leave loading, and notice — and that their termination was reported through STP. Our guides on how to calculate final pay and how to terminate an employee cover the entitlements auditors check first.
How RosterElf supports audit preparation
RosterElf’s integrated platform simplifies EOFY preparation.
Automatic reconciliation
Timesheet data flows directly to payroll export, eliminating manual reconciliation. Variance reports highlight any discrepancies instantly for investigation.
Award compliance built-in
Correct penalty rates, loadings, and minimum engagement periods are applied automatically based on shift times and employee classifications.
Complete audit trail
Every roster, timesheet, and approval is timestamped and stored. Generate complete records for any period instantly when needed for audit.
Comprehensive reporting
Run reports by employee, period, cost centre, or location. Export data in formats compatible with accounting software and auditor requirements.
Real-time accuracy
Issues are identified as they occur, not months later. Real-time validation means fewer corrections needed at EOFY.
Payroll integration
Smooth export to Xero, MYOB, and other systems. Data integrity is maintained throughout the process without manual re-entry errors.
Related RosterElf features
Prepare for EOFY with confidence. RosterElf helps Australian businesses keep audit-ready records with integrated time tracking, automatic timesheet-to-payroll reconciliation, built-in award compliance, and a complete audit trail — with a clean export to Xero and MYOB.
Disclaimer
This article provides general guidance only and does not constitute financial, tax, or legal advice. Payroll and tax requirements change regularly. Always verify current requirements with the Australian Taxation Office and consult qualified professionals for specific business decisions.
Frequently asked questions
What should you check in payroll before EOFY?
Before EOFY, verify all employee details are current — including TFN declarations, superannuation fund details, and tax withholding rates. Reconcile all pay runs against timesheets and rosters. Check that all allowances, penalty rates, and overtime have been calculated correctly. Ensure leave balances are accurate and any accruals are properly recorded, and reconcile superannuation contributions against ATO requirements.
How do you prepare for a payroll audit in Australia?
Prepare for a payroll audit by organising all payroll records — timesheets, rosters, pay slips, and tax documentation — and keeping them accessible for at least 7 years as required by Fair Work. Verify award compliance by checking pay rates against current award rates, document your payroll processes and exceptions, and run reconciliation reports comparing rostered hours to paid hours. Our guide on how to conduct a payroll audit walks through the full process.
What payroll records must employers keep in Australia?
Australian employers must keep employee records for 7 years, including time and wages records, leave records, superannuation contribution records, tax file declarations, and pay slips. Payroll records must show hours worked, pay rates, deductions, superannuation contributions, and any allowances or loadings paid.
What are common payroll audit findings?
Common findings include incorrect award classification, underpayment of penalty rates, missing or incorrect superannuation contributions, inaccurate overtime calculations, failure to pay minimum engagement periods for casuals, and discrepancies between rostered and paid hours. Automated award interpretation prevents most of the rate-related errors before they happen.
When should EOFY payroll preparation start?
EOFY payroll preparation should start at least 8-12 weeks before 30 June. This allows time to identify and correct discrepancies, update employee details, reconcile superannuation, and ensure all pay runs are processed accurately. Starting early avoids the rush and reduces the risk of errors in final payments.
What is the STP finalisation deadline for EOFY?
Employers must lodge their Single Touch Payroll finalisation declaration by 14 July for most employees. Lodging finalises each employee’s year-to-date payroll data and releases their income statement in myGov. Before you lodge, reconcile your STP-reported totals against your actual pay runs so the figures match — our guide on how to complete EOFY payroll covers the finalisation steps in order.
When does superannuation need to be paid before EOFY?
To claim a tax deduction in the current financial year, super contributions must be received by employees’ funds — not just sent from your account — by 30 June, so allow around two weeks’ clearing time. The final quarterly super guarantee payment for the year is due by 28 July. From 1 July 2026, payday super requires super to reach funds within 7 business days of each pay run.
How do you reconcile payroll with timesheets?
Reconcile payroll with timesheets by comparing total hours recorded in timesheets against hours paid in each pay run. Check that penalty rates were applied for the correct periods and that overtime calculations match timesheet records. Investigate any variances — manual adjustments, rounding, or data-entry errors. Time and attendance integrated with payroll removes most of this manual comparison.
How do integrated payroll systems help with audit preparation?
Integrated payroll systems automatically reconcile timesheets to pay runs, apply correct award rates and penalties, and keep a complete audit trail of every change. Reports can be generated instantly for any audit period, and real-time data means fewer end-of-year corrections are needed. This turns reconciling payroll into a quick review rather than a manual rebuild.
