It’s that time of year again. But before you pop the champagne for another EOFY wrap, let’s make sure your payroll house is in order. The ATO expects precision, but if your payroll doesn’t match your records, you’re not just risking a few headaches; you could be exposing your business to penalties, employee complaints and a lot of unnecessary admin cleanup.

 

here’s what every business needs to lock down before + just after 30 June:

 

STP finalisation – due 14 July 2025

You must declare your payroll year is final via Single Touch Payroll [STP] by 14 July. This allows your employees to see their ‘tax ready’ income statements in myGov.

Don’t hit ‘finalise’ too soon. Check that gross wages, PAYG withholding and super in your payroll system reconcile with your general ledger and BAS. Mismatches trigger ATO data-matching alerts and audits.

 

superannuation guarantee – due 28 July [but pay early!]

Technically, Quarter 4 super isn’t due until 28 July 2025, but if you want the deduction in FY25, it must clear the employee’s fund by 30 June.

Don’t risk cutting it close. Super clearing houses need time to process payments. If it lands in July, you’ll lose the deduction.

 

reportable employer super contributions [RESC]

Any additional super [like salary sacrifice or employer top-ups] must be properly classified as reportable employer superannuation contributions [RESC] in your STP finalisation. If it’s incorrectly reported, it can throw off your employee’s tax return or government entitlements.

 

fringe benefits tax [FBT] + RFBA

If you’ve provided perks like cars or gym memberships, you may need to report Reportable Fringe Benefits Amounts [RFBA] for employees receiving over $2,000 in fringe benefits.

  • FBT return [via tax agent]: Due 25 June 2025
  • RFBA via STP: Due 14 July 2025

Make sure the figures align between your FBT return and payroll system.

 

reconciliation is everything

Your EOFY payroll numbers should match:

  • General ledger [wages, PAYG, super]
  • STP lodgements
  • BAS reports
  • Super clearing house data
  • FBT disclosures [if applicable]

If something doesn’t tie out, fix it now, not after the ATO comes knocking.

 

payroll tax and PAYG withholding

  • Annual payroll tax reconciliation is due 28 July 2025 in most states if you’re above the wage threshold.
  • Ensure your PAYG withholding lodged in STP matches what was reported in your BAS throughout the year.

The ATO cross-checks everything. Don’t give them a reason to question your records.

 

review leave + backup your data

Check for excessive leave balances. Anything over 8+ weeks might need a conversation — and financial provisioning.

Back up all your EOFY reports: STP finalisations, super payments and reconciliations. The ATO requires you to keep payroll records for at least 5 years.

 

review your payroll setup

EOFY is the perfect time to ask:

  • Is your software saving time or causing errors?
  • Is there an opportunity for more automation?
  • Are your pay rates in line with minimum awards?

 

If your payroll system is clunky or inconsistent, now’s the time to fix it before another year rolls in.

 

wrapping up FY25 the right way

 

EOFY isn’t just a compliance exercise, it’s a credibility opportunity. Accurate payroll builds trust with your team and keeps you off the ATO’s radar.

Once payroll’s locked down, take a step back and look at the bigger picture. Here are 7 things smart businesses and their bookkeepers are doing to set themselves up for a stronger FY26.

 

get in touch

If you’re unsure, overwhelmed, or just want a second pair of eyes, the businessDEPOT bookkeeping experts are here to help. We’ll get you ATO-ready and help set you up for a cleaner FY26.

 

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