How to complete EOFY payroll in Australia
A complete guide to end of financial year payroll processing in Australia — covering STP finalisation, superannuation deadlines, reconciliation, and preparing for the new financial year.
Written by
Georgia Morgan
General information only – not legal advice
This guide provides general information about EOFY payroll processing in Australia and does not constitute financial or tax advice. Consult your accountant or registered tax agent for advice specific to your situation. It does not constitute legal, HR, or professional advice and should not be relied on as a substitute for advice specific to your business, workforce, or circumstances.
Quick start: three things to do first
Process all pay runs before 30 June. Every pay event must be lodged with the ATO via STP and dated on or before 30 June. Use integrated payroll software to reconcile automatically.
Pay super early. Super must be received by the fund by 28 June to be tax deductible this financial year. Submit your clearing house payment by 23 June to allow for bank clearing time.
Submit STP finalisation by 14 July. File the declaration through your payroll software. Once submitted, employees can access their income statement as "Tax ready" in myGov and complete their tax return.
2025–26 super rate update: From 1 July 2025, the Super Guarantee rate is 12% (up from 11.5%). Check your payroll software settings before processing any July pay runs — paying at 11.5% is a compliance breach.
EOFY payroll key dates
23 June
Submit super payments to clearing house for EOFY tax deductibility (allows bank clearing time)
28 June
Super contributions must be received by funds for tax deductibility in the current financial year
30 June
End of financial year — all pay runs must be dated on or before this date
1 July
New tax tables, award rates, and 12% super guarantee rate take effect
14 July
STP finalisation declaration due to ATO for arm's-length employees
21 July
June quarter super guarantee due to funds
30 September
STP finalisation deadline for closely held payees (family members, directors, shareholders)
31 October
Tax returns due without a tax agent
7 steps to complete EOFY payroll
Follow these steps in order to ensure compliant EOFY payroll processing.
Finalise all pay runs for the financial year
Ensure every pay event from 1 July to 30 June is processed, dated correctly, and successfully lodged with the ATO via STP.
Key actions:
- All pay runs must be dated on or before 30 June — pay events dated 1 July onwards belong to the new financial year
- Check that every STP submission shows "Accepted" in your payroll software (rejected or pending reports must be resubmitted)
- Use your payroll reconciliation report to confirm no pay runs are missing
- Process any outstanding amendments before submitting the finalisation declaration
Reconcile payroll data against ATO records
Compare your payroll register and activity reports against the ATO's year-to-date figures to confirm everything matches before finalisation.
Key actions:
- Run a payroll summary report for the full financial year and compare gross wages, PAYG withholding, and superannuation against ATO pre-fill data
- Check that allowances are correctly categorised — travel, tools, and other allowances must be itemised separately under STP Phase 2
- Verify that reportable employer superannuation contributions (RESC) are included if applicable
- Download your YTD verification report from the ATO Business Portal to cross-reference figures
Update employee details and termination records
Verify all employee information is current and that ceased employees have been correctly processed in your payroll system.
Key actions:
- Confirm tax file numbers (TFNs), addresses, and employment basis codes (full-time, part-time, casual) are up to date
- Terminated employees must be finalised in STP within 14 days of their last payment — see our guide on how to terminate an employee
- Check cessation reason codes are correct — the ATO uses these to determine entitlement to certain payments
- Issue an employment separation certificate to any employee who requests one for Centrelink purposes
Confirm superannuation payments
Ensure all super contributions are paid and received by the fund in time to meet tax deductibility and compliance requirements.
Key actions:
- Super must be received by the fund by 28 June for tax deductibility — submit to your clearing house by 23 June to allow clearing time
- The Super Guarantee rate is 12% from 1 July 2025 — verify your payroll settings are updated before processing any July pay runs
- Check all employee super fund details (fund name, USI, member number) are current — payments to incorrect funds may not satisfy the SG obligation
- Document any super guarantee charge (SGC) obligations if contributions were paid late — SGC is not tax deductible and attracts additional interest and fees
Review fringe benefits and reportable amounts
Check whether you need to report fringe benefits or other reportable amounts in your STP finalisation before submitting.
Key actions:
- If you provided reportable fringe benefits (RFBA), calculate the grossed-up taxable value and include it in the STP finalisation
- Reportable employer super contributions (RESC) — amounts above the SG minimum — must be separately reported in STP
- FBT is calculated on benefits provided between 1 April and 31 March — the FBT year differs from the income year, so check with your accountant
- Employees with RFBA or RESC amounts will see these on their income statement and must declare them in their tax return
Submit STP finalisation declaration
File your finalisation declaration through your payroll software by 14 July to confirm all payroll data is tax-ready for employees.
Key actions:
- In Xero: go to Payroll → Single Touch Payroll → EOFY finalisation → select year → Submit
- In MYOB: go to Payroll → Single Touch Payroll reporting → EOFY finalisation tab → select employees → Notify ATO
- Once submitted, employees can access their income statement as "Tax ready" in myGov — they cannot lodge their tax return until this is done
- Closely held payees (family members of trusts, directors, shareholders) have an extended deadline of 30 September — report their amounts quarterly
Prepare for the new financial year
Update your payroll system before processing the first pay run of the 2025–26 financial year to ensure compliance from day one.
Key actions:
- Update tax tables for new PAYG withholding rates — your payroll software should prompt you on 1 July
- Confirm the super guarantee rate is set to 12% for all employees
- Apply annual wage review increases from the first full pay period on or after 1 July — check your award rates for the specific effective date
- Update public holiday dates and any other calendar settings in your rostering system for the new financial year
RosterElf integrates with Xero and MYOB — approved timesheets push directly to payroll, making EOFY reconciliation faster and reducing manual errors.
See payroll integrationEOFY payroll checklist
Use this checklist to confirm you've completed all EOFY requirements before and after 30 June.
All pay runs processed and lodged with ATO (STP accepted)
YTD totals reconciled for all employees
Terminated employees finalised in STP within 14 days
Super contributions received by fund by 28 June
Super fund details verified for all employees
Super guarantee rate confirmed at 12% for July 2025 onwards
Reportable fringe benefits (RFBA) calculated and included
STP finalisation declaration submitted by 14 July
Employee income statements marked "Tax ready"
Tax tables updated for new financial year
Award rates updated for 1 July increases
Public holidays updated in rostering system
Superannuation at EOFY
Super guarantee rate from 1 July 2025: 12%
This is the final legislated rate — it will remain at 12% permanently. Update your payroll software settings before processing the first pay run of the 2025–26 financial year.
Tax deductibility deadline
Super must be received by the fund by 30 June. Submit to your clearing house by 23 June to allow for bank clearing time (typically 3–5 business days).
Late payment consequences (SGC)
Late contributions attract the Super Guarantee Charge: unpaid amount + 10% p.a. interest + $20 admin fee per employee per quarter. The SGC is not tax deductible.
Key STP phase 2 super reporting codes
| Element | Description | Code |
|---|---|---|
| Superannuation | Super guarantee and salary sacrifice contributions | SUP |
| Reportable fringe benefits | Grossed-up taxable value of FBT amounts | RFB |
| PAYG withholding | Tax withheld from employee payments | PTW |
| Gross payments | Total gross wages before deductions | GAP |
For the complete super guarantee history and rate schedule, see our superannuation guarantee glossary.
Common EOFY payroll mistakes
Avoid these costly errors during EOFY processing.
Missing the super payment deadline
Consequence: Super paid after 28 June is not tax deductible in the current year and attracts the Super Guarantee Charge (SGC)
Solution: Submit super payments by 23 June to allow for bank clearing times. Set a calendar reminder 2 weeks before EOFY.
Forgetting terminated employees
Consequence: Former employees cannot lodge tax returns until their income statement is finalised — this creates legal exposure
Solution: Finalise terminated employees in STP within 14 days of their last pay — do not wait until July.
Not updating payroll settings on 1 July
Consequence: Incorrect PAYG withholding and super rates from the start of the new financial year — employees may be underpaid super
Solution: Before the first July pay run, update tax tables, confirm super is set to 12%, and apply award rate increases.
Ignoring STP amendments
Consequence: Employees receive incorrect pre-fill data in their tax returns, leading to disputes and ATO correspondence
Solution: Review and amend any STP errors or rejected submissions before submitting the finalisation declaration.
Missing the 14 July deadline
Consequence: ATO penalties up to $16,500 per breach for STP non-compliance — and your employees are blocked from completing tax returns
Solution: Apply for a deferral before 14 July if you genuinely cannot meet the deadline. Do not ignore the deadline.
Regulatory sources
This guide is aligned with official Australian tax, payroll, and super regulations. Key references:
Related guides
More resources for payroll processing and compliance.
Automate payroll compliance
RosterElf integrates with Xero and MYOB to keep your payroll accurate year-round — making EOFY reconciliation and STP finalisation straightforward.
Frequently asked questions
- STP (Single Touch Payroll) finalisation is the process of confirming to the ATO that all payroll information for the financial year is complete and correct. Once finalised, employees can see their income statement as "Tax ready" in myGov and use it for their tax return. STP replaced the old payment summary system — you no longer need to issue Group Certificates.
- The deadline is 14 July each year for arm's-length employees. For example, STP finalisation for the 2024–25 financial year must be submitted by 14 July 2025. Closely held payees (family members, directors, shareholders) have until 30 September. If you cannot meet the deadline, apply to the ATO for a deferral before 14 July.
- Yes — contact the ATO before 14 July to apply for a deferral. Extensions are typically granted for genuine hardship, natural disasters, or technical issues with payroll software. Apply through ATO Online Services or your registered tax agent. Applying for a deferral does not exempt you from penalties if STP finalisation is never submitted.
- No. STP has replaced payment summaries for most employers. Employees access their income statement through myGov once you submit your finalisation declaration. However, you may still need to issue a payment summary for reportable employer superannuation contributions (RESC) in certain circumstances — check with your accountant if unsure.
- The ATO may apply penalties of up to $16,500 per breach for STP non-compliance. More importantly, your employees cannot see their finalised income information to complete their tax returns until you submit the declaration — this affects their ability to receive any tax refund.