STP EOFY Finalisation in Australia 2026: A Bookkeeper's Complete Guide for Employers

For Australian employers and their bookkeepers, the end of the financial year brings one of the most time-sensitive compliance obligations in the payroll calendar: Single Touch Payroll (STP) finalisation. With the 2025–26 financial year now closed, the ATO requires all employers to submit their STP finalisation declaration by 14 July 2026. Missing this deadline can delay employees' tax returns, attract ATO scrutiny, and expose businesses to penalties. A skilled bookkeeper is the frontline professional who ensures this process runs smoothly, accurately, and on time.

Understanding STP Finalisation

Single Touch Payroll is the ATO's real-time payroll reporting framework, requiring employers to report wages, tax withheld, and superannuation information to the ATO each time they run a payroll. At the end of each financial year, employers must submit a finalisation declaration — a formal confirmation that all payroll data for the year is complete and accurate.

Once the finalisation is submitted and accepted, employees' income statements in myGov are updated from "not tax ready" to "tax ready", enabling them to lodge their individual tax returns. This replaces the old payment summary (group certificate) system entirely. Employers are no longer required to issue paper payment summaries to employees who are reported through STP.

STP Phase 2 — which expanded the data reported to include more granular income type classifications, disaggregated allowances, and child support deductions — has been mandatory since 2023. For the 2025–26 EOFY, all employers must ensure their payroll software is fully configured for Phase 2 reporting before submitting the finalisation declaration.

Key Deadlines for 2026

Understanding the correct deadline for your business type is essential. The ATO applies different rules depending on the nature of your payees.

• Standard employees (arm's length payees): Finalisation declaration must be submitted by 14 July 2026.
• Closely held payees: For small employers (19 or fewer employees) with only closely held payees — such as family members employed in a family business — the deadline is the payee's individual tax return due date. For businesses with both arm's length and closely held employees, the closely held payee deadline is 30 September 2026.
• Deferrals: If an employer cannot meet the standard deadline, they must apply to the ATO for a formal deferral before 14 July 2026. Registered BAS agents and tax agents managing payroll on behalf of clients may have access to extended lodgement schedules.

Bookkeepers who manage payroll for multiple clients should build a finalisation calendar well in advance of 14 July, prioritising clients with complex payroll structures or those who have had payroll corrections during the year.

What Bookkeepers Must Do Before Finalising

A thorough pre-finalisation reconciliation is the most critical step in the STP EOFY process. Rushing to submit without reconciling first is one of the most common — and costly — mistakes employers make.

Reconcile Year-to-Date Figures

Before submitting the finalisation declaration, bookkeepers should reconcile the following data points against the general ledger and ATO records:

• Gross wages and salaries — Ensure total YTD gross pay in the payroll system matches the wages expense account in the general ledger.
• PAYG withholding — Reconcile total tax withheld reported through STP against the amounts remitted to the ATO via Business Activity Statements (BAS) throughout the year.
• Superannuation contributions — Verify that all super liabilities have been calculated correctly and that contributions have been paid to the relevant funds. From 1 July 2026, Payday Super requires super to be paid at the same time as wages, so any outstanding contributions from the 2025–26 year must be addressed promptly.
• Allowances and fringe benefits — Confirm that all allowances (e.g., car, travel, tool allowances) are correctly classified under STP Phase 2 income type codes, and that reportable fringe benefits amounts (RFBAs) are accurately reflected.
• Terminated employees — Ensure all employees who left during the 2025–26 year are included in the finalisation, with correct termination dates and final pay details.

Check Payroll Software Configuration

Payroll software must be fully configured for STP Phase 2 before the finalisation is submitted. Bookkeepers should confirm that income type classifications, country codes for working holiday makers, and child support garnishee amounts are correctly mapped in the system.

Common software platforms used by Australian bookkeepers — including Xero, MYOB, QuickBooks, and KeyPay — all support STP Phase 2 finalisation. However, the specific steps for submitting the finalisation declaration vary between platforms, and bookkeepers should follow the software provider's EOFY guide for the 2025–26 year.

Common Mistakes and Red Flags

Even experienced bookkeepers can encounter pitfalls during STP finalisation. Being aware of the most common errors helps prevent costly amendments and ATO follow-up.

• Submitting before all pay runs are processed: If a late pay run or correction is processed after the finalisation is submitted, an amended finalisation declaration must be lodged. Always confirm that every pay run for the financial year — including any June 2026 pay runs processed in early July — has been reported before finalising.
• Incorrect income type classifications: STP Phase 2 requires employers to classify income by type (e.g., salary and wages, closely held payee income, working holiday maker income). Misclassification can cause discrepancies in employees' pre-fill data and trigger ATO queries.
• Forgetting reportable employer super contributions (RESCs): If an employer makes super contributions above the minimum Superannuation Guarantee (SG) rate at the employee's direction, these must be reported as RESCs. Omitting RESCs can affect employees' tax return calculations.
• Not obtaining client authority: Bookkeepers acting as registered BAS agents should obtain a signed authority from the client before submitting the finalisation declaration on their behalf. This protects both the bookkeeper and the client in the event of a dispute.
• Ignoring ATO error messages: If the ATO rejects a finalisation submission, the error message must be investigated and resolved before resubmitting. Common rejection reasons include mismatched TFNs, duplicate submissions, and invalid income type codes.

Australian Regulatory Context

STP finalisation obligations are governed by the Taxation Administration Act 1953 and the ATO's STP reporting framework. The ATO has broad powers to issue penalties for late or inaccurate finalisation declarations, though it generally takes a practical approach for first-time or minor errors where the employer has made a genuine attempt to comply.

Bookkeepers who are registered as BAS agents with the Tax Practitioners Board (TPB) are authorised to prepare and lodge STP finalisation declarations on behalf of their clients. This registration requires meeting ongoing continuing professional education (CPE) requirements and adhering to the TPB's Code of Professional Conduct. Unregistered bookkeepers cannot legally provide BAS services, including STP finalisation, for a fee.

The ATO's Online services for agents portal provides BAS agents with visibility over their clients' STP reporting status, enabling bookkeepers to identify any outstanding or rejected submissions before the 14 July deadline. The ATO also publishes an annual EOFY guide for employers and agents, which is updated each year to reflect any changes to reporting requirements.

Looking ahead, the commencement of Payday Super from 1 July 2026 will significantly increase the complexity of payroll compliance. Under Payday Super, employers must pay superannuation contributions at the same time as wages, and the ATO will use STP data to cross-match super liabilities with fund receipts in near real-time. Bookkeepers who manage payroll for their clients will need to ensure their systems and processes are updated to meet these new obligations from the start of the 2026–27 financial year.

Questions to Ask When Choosing a Bookkeeper for STP Compliance

If you are an employer looking for a bookkeeper to manage your STP obligations — including EOFY finalisation — the following questions will help you identify a qualified and capable professional.

• Are you a registered BAS agent with the TPB? Only registered BAS agents can legally provide STP finalisation services for a fee. Ask to see their TPB registration number.
• Which payroll software do you use, and are you certified in it? Xero, MYOB, and QuickBooks all offer partner or advisor certifications. A certified bookkeeper will be more efficient and less likely to make software-related errors.
• How do you handle STP Phase 2 income type classifications? A knowledgeable bookkeeper should be able to explain the different income types and how they apply to your workforce.
• What is your process for reconciling payroll before finalisation? Look for a structured, documented reconciliation process rather than a bookkeeper who simply clicks "submit" without checking the numbers.
• How will you handle Payday Super from 1 July 2026? This is a significant change, and your bookkeeper should have a clear plan for updating your payroll processes to comply.
• What are your fees for EOFY finalisation? Some bookkeepers charge a flat fee for EOFY services; others include it in a monthly retainer. Understand what is included before engaging.

How MyMoney® Can Help

Finding a qualified, TPB-registered bookkeeper who understands STP Phase 2, EOFY finalisation, and the upcoming Payday Super changes can be challenging — especially for small business owners who are already stretched at year-end.

MyMoney® connects Australian employers with experienced, vetted bookkeepers who specialise in payroll compliance, STP reporting, and BAS services. Whether you need a bookkeeper to manage your entire payroll function or simply to handle the annual EOFY finalisation, our marketplace makes it easy to find the right professional for your business.

Post a Brief to describe your payroll needs and receive tailored proposals from qualified bookkeepers in your area. Or Browse Bookkeepers to explore profiles, qualifications, and client reviews. With the 14 July 2026 deadline approaching, now is the time to ensure your STP finalisation is in expert hands.