Xero payroll: checks before and after every pay run

A Xero payroll run can look finished while an important step is still open. This Australian checklist defines what counts as done: wages, payslips, Single Touch Payroll (STP) and super each need their own record.

The short answer: check the inputs, approve the amounts and verify each outcome separately. Keep a named reviewer and a piece of evidence beside every check, and stop when the evidence is missing.

Check the settings before the totals

Xero says you can “review and approve each pay run”.¹ Its reply to a request for automatic award rates says it has no “immediate plans to build this directly into Xero Payroll”.² Confirm classifications and rates with your payroll adviser, or with the award software you connect.

Leave needs its own check. The Fair Work Act gives 4 weeks of paid annual leave a year, or 5 for qualifying shiftworkers. It accrues by ordinary hours, and casual employees are outside it.³ Xero’s payroll guide also lists wrong tax rates and forgotten leave accruals among common mistakes.⁴ Check timesheets and job hours before copying figures between systems.

Work through a sample pay run

Sample data, not a client’s. PAYG is assumed, all gross pay counts as qualifying earnings and no other deductions apply. Employer super sits outside net wages. The Payday Super Act inserts section 17A into the Superannuation Guarantee (Administration) Act 1992. It sets the individual superannuation guarantee amount as the qualifying earnings multiplied by the charge percentage over 100, and says “charge percentage means 12”.⁶ Xero’s guide to qualifying earnings gives the same rate.⁵ Confirm earnings treatment with your adviser.

Keep a stop and go control sheet

Keep unexplained differences open. Record the resolution and restrict access to payroll evidence. This is a working checklist, not a guarantee, so test it on a completed pay cycle first.

Finish each payment and report

The Fair Work Act requires a pay slip “within one working day of paying an amount to the employee in relation to the performance of work”.³ For super, the Payday Super Act sets a usual period. It ends on the seventh business day after qualifying earnings are paid, and an “extended usual period” of 20 business days applies in some cases.⁶ MYOB says payments “must reach the super funds within 7 business days of payday”.⁷

STP is a separate outcome. Keep the submission and its response with the pay run, and confirm the applicable deadline and any concession with your adviser. This checklist covers the whole pay run, from inputs to reconciliation; the Payday Super pay-run check follows one super payment from payroll to the fund.

Keep MYOB corrections separate

MYOB’s help says whether you can delete or reverse a pay is “based on its status in the STP Payroll Reporting Centre”. It adds that you should only do so if the amount has not left your bank account.⁸ MYOB also says super payments “start processing only after authorisation”.⁷ For Xero corrections, follow Xero’s support pages and your adviser’s instructions.

Where a person stays in charge

I would build around approved exports and documented checks, with an n8n workflow comparing totals and dates. A person confirms treatment, approves, lodges and pays. This is a Custom build, from A$9,500 (AUD, no GST charged).⁹

Start with a free fit check by email at the foot of this page. If you are not sure which checks come first, the next step is a Workflow Audit for A$990 (AUD, no GST charged).⁹ It is a 60-minute call, a read-only review of your systems and a written report, with a fixed quote for each of the top 3 things worth automating. This is general information, read on 31 October 2026. Get payroll or tax advice for your circumstances, especially corrections and uncertain entitlements.

Questions

Sources

• 1. Xero, “Payroll software for Australia”, read 31 October 2026: xero.com/au/accounting-software/payroll
• 2. Xero Product Ideas, “AU Payroll: Setting award wages automatically”, official response of 24 February 2026, read 31 October 2026: productideas.xero.com/…/45389275-au-payroll-setting-award-wages-automatically
• 3. Federal Register of Legislation, “Fair Work Act 2009”, sections 86, 87 and 536, compilation of 7 July 2026, read 31 October 2026: legislation.gov.au/C2009A00028/latest/text
• 4. Xero, “Small business payroll: steps, compliance and software” (published 22 October 2026), read 31 October 2026: xero.com/au/guides/small-business-payroll
• 5. Xero, “Qualifying earnings and Payday Super” (published 25 July 2026), read 31 October 2026: xero.com/au/guides/qualifying-earnings-payday-super
• 6. Federal Register of Legislation, “Treasury Laws Amendment (Payday Superannuation) Act 2025” (C2025A00057, as made 6 November 2025), read 31 October 2026: legislation.gov.au/C2025A00057/asmade/2025-11-06/text/1/pdf
• 7. MYOB, “Authorise and review super payments”, read 31 October 2026: myob.com/au/support/myob-business/payroll/…/authorise-and-review-super-payments
• 8. MYOB, “Fixing a pay”, read 31 October 2026: myob.com/au/support/myob-business/payroll/processing-your-payroll/fixing-a-pay
• 9. Works Better, “Pricing” and “Workflow Audit”: worksbetter.ai/pricing (Custom build from A$9,500; Workflow Audit A$990; AUD, no GST charged)