EOFY 2025 HR Checklist - 13 Days to Compliance Plus What's Coming Next
EOFY 2025 HR compliance checklist for Australian employers: super payment deadlines, STP finalisation, wage increases and the move to Payday Super.
Updated October 2026: This checklist was written for EOFY 2025. Payday Super started on 1 July 2026: super is now due with every pay run and must reach the employee's fund within 7 business days of payday, and the super guarantee charge for paydays from 1 July 2026 is tax deductible. The 12% super rate has applied to earnings paid since 1 July 2025. We have corrected the super, penalty and pay-run details below. Read Payday Super from 1 July 2026: what employers need to do.
Key compliance deadlines every Australian SMB must meet
With $3.4 billion in unpaid superannuation affecting Australian workers annually, the ATO is intensifying enforcement this EOFY. The most critical deadline isn't 30 June — it's 23 June 2025, when super payments must be submitted to ensure they're received by funds in time for tax deductions.
Missing this date could cost your business thousands in penalties and lost deductions.
Australian SMBs face a perfect storm of compliance requirements over the next two weeks. You need to finalise payroll, meet super deadlines, implement a 3.5% minimum wage increase, and prepare for the most significant super reform in decades.
This comprehensive guide breaks down exactly what you need to do, when you need to do it, and how to avoid the costly mistakes that catch out 1 in 4 businesses every year.
Understanding EOFY compliance requirements
End of Financial Year (EOFY) compliance encompasses all the legal obligations employers must meet to properly close their books and remain compliant with Australian employment law. For HR and payroll, this means ensuring all employee payments, entitlements, and records are accurate, up-to-date, and properly reported to the Australian Taxation Office (ATO) through Single Touch Payroll (STP).
Under the Fair Work Act 2009 and taxation legislation, employers must maintain accurate records of all employee payments, superannuation contributions, and leave entitlements. The Fair Work Act requires employee records to be kept for seven years (tax records for at least five), with significant penalties for non-compliance.
Beyond basic record-keeping, EOFY triggers specific deadlines for super payments, STP finalisation, and preparation for new financial year changes including award rate increases.
What makes 2025 particularly challenging is the convergence of multiple reforms. Criminal penalties for wage theft came into effect in January, STP Phase 2 reporting is now mandatory for all employers, and we're on the cusp of the biggest superannuation reform since compulsory super began — Payday Super, launching 1 July 2026.
EOFY legal obligations for employers
Meeting your EOFY compliance obligations requires careful attention to multiple deadlines and requirements. Understanding these important obligations protects your business from penalties while ensuring proper employee entitlements.
Critical Deadline - 23 June 2025
To claim tax deductions for super contributions in FY2024-25, payments must be received and cleared by super funds by close of business 30 June. Submit electronic payments by 3:30pm AEST 23 June 2025.
Key Requirements: For 2024–25 the SG rate was 11.5% of ordinary time earnings, capped at the maximum contribution base for each quarter (since 1 July 2026 the base is an annual amount: $270,830 for 2026–27). Include all ordinary time earnings, such as base salary, commissions, shift loadings and allowances paid for ordinary hours.
Under the quarterly rules that applied until 30 June 2026, the Super Guarantee Charge for late payments included 10% p.a. interest from the start of the quarter and a $20 admin fee per employee, and it was not tax deductible. For paydays from 1 July 2026, the new charge includes notional earnings and an administrative uplift of up to 60%, and it is tax deductible.
STP Phase 2 Finalisation
All STP reports must be finalised and submitted to the ATO by 14 July 2025. This includes year-to-date totals for all employees and any amendments to previously reported data.
Phase 2 Requirements: Enhanced reporting including additional data elements, employee commencement declarations, and cessation details with specific reason codes.
Ensure your payroll software is STP Phase 2 compliant and all employee data is accurate before the deadline.
Complete Record Verification
Conduct comprehensive audits of all employee records, pay calculations, and entitlements. Verify classifications against current Modern Awards and ensure all manual adjustments are properly documented.
Focus Areas: Leave balances, overtime calculations, allowances, salary sacrifice arrangements, and terminated employee final payments.
Keep employment records for seven years as the Fair Work Act requires (tax records must be kept for at least five).
New Financial Year Changes
Implement the 3.5% minimum wage increase effective 1 July 2025, update all Modern Award rates, and apply the 12% superannuation guarantee rate to earnings paid on or after 1 July 2025.
Preparation for Payday Super: Consider transitioning to monthly super payments now to ease the eventual move to pay-cycle super contributions from 1 July 2026.
Update employment contracts, payroll systems, and employee communications to reflect new rates and obligations.
Consequences of non-compliance:
❌ Super Guarantee Charge — under the quarterly rules, 10% p.a. interest plus a $20 per employee admin fee (non-deductible); for paydays from 1 July 2026, notional earnings plus an administrative uplift of up to 60%
❌ STP non-compliance — ATO failure-to-lodge penalties for each late report, up to 5 penalty units ($1,820) for a small business and 2 or 5 times that for larger businesses
❌ Pay slip and record-keeping breaches — civil penalties of up to $21,840 per contravention for an individual and up to $109,200 (small business company) or $546,000 (other companies), for conduct from 1 July 2026, and more for serious contraventions
❌ Criminal wage theft charges — Personal liability for directors under new laws effective January 2025
How EOFY compliance impacts your business
The convergence of EOFY deadlines creates significant operational and financial impacts for Australian SMBs. Understanding these impacts helps prioritise actions and allocate resources effectively during this critical period.
| Impact Area | Immediate Effect | Long-term Consequence |
|---|---|---|
| Cash Flow | Large super payment due by 23 June | Quarterly lumps became payments with every pay run under Payday Super (from 1 July 2026) |
| Administrative Burden | Multiple deadlines within 2 weeks | Increased compliance complexity ongoing |
| Penalty Risk | SGC charges if super paid late | Criminal liability for intentional wage theft |
| Employee Relations | Questions about pay increases | Expectations of real-time super visibility |
| System Requirements | STP Phase 2 compliance needed | Payday Super system upgrades required |
Practical tips for managing EOFY compliance
Success in EOFY compliance comes from early action and systematic preparation. Focus on the most critical deadlines first, then build comprehensive processes for ongoing compliance.
✅ Submit super payments by 23 June — don't wait until 30 June. Major clearing houses and super funds recommend submission by this date to ensure funds are received and cleared for tax deduction eligibility.
✅ Run a comprehensive payroll audit (an HR compliance audit can help). Verify all employee classifications, pay rates, and entitlements are correct, and check for any manual overrides that might block automatic rate updates on 1 July.
✅ Prepare for Payday Super now by transitioning to monthly super payments. When the 12% rate applies from 1 July, you'll already have adapted to more frequent payments and smoother cash flow impact.
✅ Document everything meticulously. Create a compliance checklist with dates, amounts, and confirmation numbers for all super payments — this protects you if there are any disputes about payment timing.
✔ Build robust systems and processes to support ongoing compliance. Ensure your payroll software can handle complex scenarios and maintain proper audit trails for all payment decisions.
✔ Communicate changes early to employees about the 3.5% wage increase and new pay rates before 1 July to prevent confusion and demonstrate good faith compliance.
✔ Review and upgrade payroll systems now to handle upcoming requirements including STP Phase 2 and future Payday Super obligations.
❌ Never assume payroll software is always correct — human oversight remains critical for reviewing exception reports and checking calculations for complex scenarios.
❌ Don't mix financial years in pay runs — pay is reported in the financial year it is paid, and new award rates start from the first full pay period starting on or after 1 July. Check how your payroll system handles a pay period that spans 30 June.
Need advice on this?
Talk it through with an Employment Compass HR adviser before you act.
Final thoughts
EOFY 2025 represents a critical compliance checkpoint for Australian businesses, with the added complexity of preparing for transformative changes ahead. By acting now — particularly on the 23 June super deadline — you protect your business from penalties while positioning for smooth implementation of upcoming reforms.
Remember, compliance isn't just about avoiding penalties; it's about building trust with your employees and creating sustainable business practices. The effort you invest in EOFY compliance today sets the foundation for a successful new financial year.
With criminal penalties now applying to wage theft and Payday Super approaching, the stakes have never been higher for getting payroll compliance right.
If you need further assistance with EOFY compliance or other HR matters, our 24/7 HR Advice Line is available to all Australian business owners. Call us on 1300 144 002 today for expert advice and support tailored to your business needs.
Frequently asked questions
If super contributions don't reach and clear in the fund by 30 June, you cannot claim them as a tax deduction for the 2024-25 financial year. Under the quarterly rules that applied until 30 June 2026, missing the quarterly deadline (28 July for the June quarter) meant the Super Guarantee Charge: the unpaid amount, 10% p.a. interest from the start of the quarter and a $20 administration fee per employee, and it was not tax deductible. For paydays from 1 July 2026, the charge is tax deductible.
For STP and PAYG withholding, pay is reported in the financial year it is paid, not the year the work was done, so a pay run paid on or after 1 July belongs to the new financial year. Super works the same way: the rate depends on the payment date. New award and minimum wage rates apply from the first full pay period starting on or after 1 July, so a pay period that started before 1 July stays on the old rates. Check your payroll settings.
Every payslip must include the employer's name and ABN, the employee's name, the pay period, the payment date, gross and net amounts, and any loadings (including casual loading), allowances, bonuses and penalty rates. Also show each deduction and the fund or account it was paid to, super contributions and the fund, and, for hourly-paid employees, the ordinary hourly rate, hours worked at that rate and the amount (for salaried employees, the annual rate). Payslips must be provided within one working day of payment.
Now, if you haven't already: Payday Super started on 1 July 2026. Super must be paid with each pay run and reach the employee's fund within 7 business days of payday (20 business days in limited cases, such as a new employee's first contribution). Check that your payroll software and clearing house can meet the deadline, and plan cash flow for 12% super on every pay run, whatever your pay cycle.
Late super payment deductibility depends on timing. If you pay after 30 June but before the quarterly deadline (28 July), the payment is deductible in the financial year it's received by the fund — so it would be a FY2025-26 deduction, not FY2024-25. Under the quarterly rules that applied until 30 June 2026, if you missed the quarterly deadline and incurred the Super Guarantee Charge, the SGC was not tax deductible. For paydays from 1 July 2026 the new SGC is tax deductible, but late payment still costs you notional earnings and an administrative uplift of up to 60%.
Since 1 January 2025, intentional wage underpayment became a criminal offence under the Fair Work Act. It applies when an employer intentionally engages in conduct that results in an underpayment. Penalties include up to 10 years' imprisonment for individuals, and fines of up to the greater of 3 times the underpayment or $9.1 million for companies (conduct from 1 July 2026). Directors and senior managers can be held personally liable if they knew about or were wilfully blind to underpayments, reinforcing the importance of accurate payroll systems and immediate correction of errors.
General information only
This content is general information about Australian employment law, current at the date it was last reviewed. It does not take your circumstances into account and is not legal advice. For advice about your situation, call Employment Compass on 1300 144 002.
Last reviewed: October 2026
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Every workplace is different. For advice on how this applies to your business, call our 24/7 HR advice line and speak with an Employment Compass HR adviser.
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