EOFY Payroll and Super Obligations: What Australian Small Business Owners Need to Know

If you employ people in Australia, the end of financial year brings a specific set of payroll and superannuation obligations on top of your regular tax prep. Miss them and you risk ATO penalties, unhappy employees, and a messy start to the new financial year.

This guide walks through everything you need to do before and after June 30: and how AI tools can help you stay on top of it.

1. Single Touch Payroll (STP) Finalisation

Single Touch Payroll is the ATO’s system for real-time payroll reporting. Every time you pay your employees, the data is sent directly to the ATO via your payroll software.

At EOFY, you must “finalise” your STP data. This tells the ATO that the year-to-date figures for each employee are correct and complete. Once finalised, employees can access their income statement through myGov to lodge their own tax returns.

Deadline: 14 July 2026 (for most employers). Some small employers may have an extended deadline: check with your payroll software or the ATO.

How to do it:

• Xero Payroll: go to Payroll → Payment Summaries → mark as final for each employee
• MYOB AccountRight. Payroll → Single Touch Payroll → Finalise
• KeyPay / Employment Hero Payroll: similar process in the STP section
• If you use a bookkeeper or payroll bureau: remind them the deadline is 14 July

How AI helps: If you’re unsure about the process in your specific software, ask ChatGPT: “Walk me through how to finalise STP for FY2025–26 in [software name].” It will give you a step-by-step walkthrough.

2. Super Guarantee: Q4 Contributions

The Superannuation Guarantee (SG) rate for FY2025–26 is 11.5%. From 1 July 2026, it increases to 12%: the final step in the legislated schedule to reach 12%.

Q4 super (April–June) is due 28 July 2026. However, if you want to claim the contribution as a deduction in FY2025–26, you must pay it before 30 June 2026.

This is one of the simplest and most powerful tax planning moves available to employers: pay your Q4 super a month early, claim the deduction this financial year.

Important: Super contributions are deductible when they’re received by the super fund: not when you transfer the money. If you use a clearing house (like the ATO’s Small Business Superannuation Clearing House), allow extra processing time. Aim to submit by mid-June to be safe.

Super Rate Change from July 2026

From 1 July 2026, the SG rate increases from 11.5% to 12%. Make sure your payroll software is updated to apply the new rate from the first pay run in July. Most major platforms (Xero, MYOB, Employment Hero) update this automatically: but it’s worth checking.

Prompt to try:

“I have 4 employees with the following gross wages in Q4: [list]. Calculate the superannuation guarantee at 11.5% for each employee and the total I need to pay.”

3. Review Your Payroll Records

Before you finalise STP, review your payroll records for the full year:

• Are all pay runs recorded correctly?
• Have leave entitlements been tracked (annual leave, sick leave)?
• Were any termination payments processed correctly?
• Were any allowances (car, meal, uniform) reported correctly?
• Were any contractor payments made that should have been employee payments (worker misclassification is an ATO audit target)?

How AI helps: Use ChatGPT to generate a payroll audit checklist for your specific situation: “I have [X] full-time and [Y] casual employees in [industry]. Generate an EOFY payroll audit checklist for me.”

4. Check Contractor vs. Employee Status

The ATO has been actively cracking down on sham contracting: where workers are treated as contractors but legally should be employees. If you use contractors, EOFY is a good time to review their status.

The key tests look at: control over work, provision of equipment, ability to sub-contract, risk of profit/loss, and integration into the business.

How AI helps: Ask ChatGPT to explain the ATO’s employee vs. contractor tests and apply them to your specific situation. This is a first-pass analysis: if there’s genuine uncertainty, get legal or tax advice.

5. Leave Liabilities and Provisions

Your employees’ accrued leave is a liability on your balance sheet. At EOFY, make sure:

• Annual leave balances are accurate in your payroll system
• Long service leave has been tracked (generally accrues after 7 years, rules vary by state)
• If any employees have excessive leave balances, consider requiring them to take leave: high leave liabilities are a financial risk

Modern payroll software handles most of this automatically: but it’s worth running a leave liability report before year-end to review.

6. Prepare for the New Financial Year

Before July pay runs, make sure your payroll is set up correctly for FY2026–27:

• ☐ Update super rate to 12%
• ☐ Apply any new award wage rates (minimum wage review usually announced in June, effective 1 July)
• ☐ Review employee tax declarations (are withholding amounts still correct?)
• ☐ Check if any employees are approaching the $180,000 income threshold where higher PAYG withholding applies
• ☐ Update salary packages if you’ve committed to pay reviews

EOFY Payroll Timeline

Date	Action
Mid-June	Submit Q4 super contributions via clearing house (to ensure received by 30 June)
30 June	Process any final pay runs for the year; review leave balances
1 July	Update super rate to 12%; apply new minimum wages if required
14 July	Finalise STP: submit EOFY finalisations for all employees
28 July	Q4 super due (if not paid early)

AI Payroll Tools Worth Knowing

• Employment Hero Payroll (formerly KeyPay). Australian-built, STP-ready, handles award interpretation
• Xero Payroll: integrated with Xero accounting, popular with SMEs
• MYOB AccountRight: strong payroll features, well-suited to Australian award complexity
• Tanda: workforce management + payroll for shift-based businesses (hospitality, retail, healthcare)
• Deputy: scheduling and time tracking that connects to payroll systems

Don’t Get Caught Out

The ATO has real-time visibility into payroll via STP. Super Guarantee non-compliance is one of their most actively pursued areas: there’s no hiding missed or late super payments. If you’ve fallen behind, the ATO does have a Voluntary Disclosure process, and coming forward proactively is always better than being caught.

Get your Q4 super in early, finalise STP by 14 July, and walk into the new financial year with your payroll obligations met.

Related guides:

• 👉 EOFY AI Checklist for Australian Small Business
• 👉 AI for Tax Time: The Complete Guide
• 👉 Best AI Tools for Australian Small Business

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Sources & Further Reading

• ATO. When to Pay Super
• ATO. Super Guarantee Percentage (11.5% from 1 July 2024)
• ATO. Single Touch Payroll
• ATO. STP Finalisation by 14 July
• ATO. Super Guarantee Charge
• Fair Work Ombudsman. Paying Wages

This guide is for general information only. It does not constitute tax, legal, or financial advice. Payroll and superannuation rules change regularly: verify current rates and deadlines at ato.gov.au or with a registered accountant or payroll specialist.

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