Running a not-for-profit (NFP) organisation in Australia is rewarding, but staying compliant with the Australian Taxation Office (ATO) is crucial. Charities and NFPs must meet obligations related to income tax, GST, payroll, superannuation, and reporting.

At supertax, we help NFPs manage ATO compliance, so your organisation can focus on its mission rather than paperwork.

This FY26 ATO compliance checklist ensures your NFP is up-to-date, transparent, and fully compliant.

Why ATO Compliance Matters for NFPs

Many believe NFPs don’t pay tax, but even charities and exempt organisations have compliance obligations.

The ATO expects NFPs to:

Apply the correct tax concessions

• Report GST, PAYG, and superannuation accurately
• Keep proper financial and governance records
• Demonstrate transparency in grant and donor fund usage

Failing to comply may lead to penalties, loss of tax concessions, or reputational risk. With proper guidance from supertax, compliance becomes a tool for credibility and trust.

Step 1: Confirm Your NFP Type and Tax Status

Knowing your NFP classification determines which concessions and reporting obligations apply.

Charities:

• Registered with the ACNC
• Eligible for income tax exemption, GST concessions, and FBT rebates
• Must lodge an Annual Information Statement (AIS)

Non-charity NFPs:

• Includes sporting clubs, cultural associations, and community groups
• May be income tax exempt but require annual self-assessment
• Must lodge income tax returns if not exempt

Supertax Tip: Review your organisation type yearly to ensure your tax status and concessions remain correct.

Step 2: Income Tax Obligations

Not all NFPs are automatically exempt from income tax.

Checklist for FY26:
✔ Confirm income tax exemption status
✔ Keep written records of self-assessment
✔ Lodge income tax return if required

Supertax in Action: We ensure NFPs meet tax obligations while maximising available concessions.

Step 3: GST and BAS Reporting for NFPs

If your annual turnover is $150,000 or more, GST registration is required.

• Fundraising events may be GST-free
• GST-registered NFPs must lodge a Business Activity Statement (BAS)

Checklist for FY26:
✔ Confirm GST registration
✔ Apply GST concessions where eligible
✔ Lodge BAS quarterly or monthly
✔ Maintain compliant tax invoices

Supertax in Action: We structure accounts to clearly separate GST-free and GST-reportable income, reducing errors and saving reconciliation time.

Step 4: PAYG Withholding and Payroll Compliance

Employers in NFPs must comply with PAYG withholding and Single Touch Payroll (STP).

Checklist for FY26:
✔ Register for PAYG withholding
✔ Report via STP each pay run
✔ Remit PAYG to ATO on time
✔ Maintain accurate payroll records

Supertax in Action: Our payroll solutions ensure PAYG and STP compliance while freeing staff for mission-critical activities.

Step 5: Superannuation Guarantee

Employers must pay 12% Super Guarantee (SG) in FY26 using SuperStream.

Checklist for FY26:
✔ Pay super on time each quarter
✔ Provide choice-of-fund forms to employees
✔ Keep accurate super records

Supertax in Action: Automatic reminders and SuperStream setup prevent missed payments and penalties.

Step 6: Fringe Benefits Tax (FBT)

Salary packaging may apply to staff; some charities and PBIs are eligible for concessions.

Checklist for FY26:
✔ Review FBT concessions
✔ Record all benefits provided
✔ Lodge FBT return if applicable

supertax in Action: We coordinate FBT compliance with salary packaging providers, optimising benefits legally.

Step 7: Record Keeping and Audit Readiness

The ATO requires records to be kept for at least five years:

• Income and expenses
• PAYG and super contributions
• Board minutes and governance documents
• Grant acquittals and donor funds

Supertax in Action: We digitise records with secure systems like Xero and SharePoint, ensuring audit readiness at all times.

Step 8: ACNC Annual Reporting

Registered charities must lodge their Annual Information Statement (AIS):

Supertax in Action: We streamline AIS and financial reporting, aligning deadlines with BAS and payroll cycles.

Step 9: Trading Activities and Related Entities

Commercial activities like cafés, shops, or fundraising events may create taxable income.

Checklist for FY26:
✔ Separate trading operations from core NFP activities
✔ Assess if a separate entity is needed
✔ Ensure proper GST and income tax reporting

Supertax in Action: We advise on trading arm structure while maintaining compliance.

Step 10: Annual Compliance Review

Compliance must be reviewed every year:

• Tax status and concessions
• GST registration
• Payroll, super, and FBT obligations
• Governance and risk management

Supertax in Action: Our annual reviews ensure your NFP never misses legislative changes.

FY26 Compliance Trends for NFPs

Digital-first ATO systems: fewer paper lodgements

Increased scrutiny on FBT and salary packaging

Demand for transparency in fund usage

Director penalties for PAYG and super non-compliance

Supertax keeps NFPs up-to-date with all changes.

Your FY26 ATO Compliance Checklist for NFPs

• ✅ Confirm NFP type and tax status
• ✅ Assess income tax exemption
• ✅ Register and report GST correctly
• ✅ Meet PAYG and STP obligations
• ✅ Pay super at 12% on time
• ✅ Understand FBT and salary packaging
• ✅ Keep complete financial and governance records
• ✅ Lodge AIS and financial statements
• ✅ Review compliance annually

How supertax Supports NFPs

supertax offers:

• BAS, FBT, and income tax lodgement
• ACNC and ATO reporting assistance
• Payroll, STP, and superannuation management
• Annual compliance reviews and audit support
• Trading arm structure advice

We help NFPs stay compliant, transparent, and focused on their mission.

Final Thoughts

Compliance is critical for maintaining trust and securing funding. With Supertax, your NFP can stay compliant, credible, and focused on creating impact in FY26 and beyond.

Supertax
📧 info@mysupertax.com.au

📞 03 7074 8818
🌐 www.mysupertax.com.au