EOFY 2025 HR Checklist - 13 Days to Compliance Plus What's Coming Next

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 ATO requires these records to be kept for seven years, with significant penalties applying 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: Current SG rate 11.5% of ordinary time earnings, maximum quarterly contribution base $65,070, and include all ordinary time earnings including base salary, commissions, and allowances.

The Super Guarantee Charge applies to late payments, including 10% p.a. interest from the start of the quarter, $20 admin fee per employee, and critically — the SGC is NOT 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.

Maintain all employment records for seven years as required by the Fair Work Act and taxation legislation.

New Financial Year Changes

Implement the 3.5% minimum wage increase effective 1 July 2025, update all Modern Award rates, and prepare systems for eventual 12% superannuation rate (timeline TBA).

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 penalties — 10% p.a. interest plus $20 per employee admin fee (non-deductible)
❌ STP non-compliance — ATO penalties up to $16,500 per breach for businesses
❌ Payslip violations — Fair Work penalties up to $82,500 for serious breaches
❌ 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 become fortnightly with Payday Super
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 this week. 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 — if a pay period spans 30 June, ensure your payroll system correctly allocates earnings to the appropriate financial year.

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 Advice Line is available to all Australian business owners. Contact us on 1300 144 002 today for expert advice and support tailored to your business needs.

Frequently asked questions

What happens if superannuation doesn't reach the fund by 30 June?

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. Additionally, if you miss the quarterly payment deadline (28 July for the June quarter), you'll face the Super Guarantee Charge including the unpaid amount, 10% p.a. interest from the start of the quarter, and a $20 administration fee per employee. Critically, SGC payments are not tax-deductible.

How do I split a pay run that crosses the financial year?

When a pay period spans 30 June, you must allocate earnings to the correct financial year for accurate reporting. Most modern payroll systems handle this automatically, but verify the settings. Apportion based on days worked in each financial year and ensure your software applies the correct pay rates — old rates to pre-1 July days and new increased rates to post-1 July days. Document this split carefully for STP reporting.

What employee details must appear on every payslip?

Every payslip must include employer's name and ABN, employee's name, pay period dates, payment date, gross and net amounts, loadings, allowances, bonuses, and penalty rates. Also show all deductions with reasons, superannuation contributions, ordinary hourly rate, hours worked, and overtime details. For casual employees, indicate casual status and show casual loading separately. Payslips must be provided within one working day of payment.

When should I start preparing for Payday Super?

Start preparing immediately, even though Payday Super doesn't commence until 1 July 2026. This reform requires super to be paid with each pay run (or within 7 days), fundamentally changing cash flow patterns. Begin transitioning to monthly super payments now, review your payroll software capabilities for upgrades, and assess business cash flow to ensure you can meet fortnightly super obligations at 12% of wages.

Can I still claim tax deductions if I pay super late?

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. However, if you miss the quarterly deadline and incur the Super Guarantee Charge, the SGC itself is never tax-deductible, making timely payment critical for cash flow management.

What are the new criminal penalties for wage underpayment?

Since 1 January 2025, intentional wage underpayment became a criminal offence under the Fair Work Act. This applies when employers deliberately and systematically underpay employees, with penalties including up to 10 years imprisonment and fines up to $7.8 million for companies. 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.