Use this checklist before you finalise and pay each pay run. Each step links to the article with the full instructions.
Before the pay run
- Leave requests are submitted and approved.
- Timesheets are reviewed, work types are correct and approvals are finalised. For award or hourly employees, approved leave is converted into timesheet entries.
- New starters are fully onboarded, with tax, bank and personal details complete. Check the Sync Errors Dashboard and resolve any mismatches.
- Salary changes, cost centre changes and employment status changes (for example, casual to part-time) are finalised.
- Terminations are actioned. Final pay items, such as employment termination payments and unused leave payouts, are included on the payroll changes form.
- The pay schedule and pay period dates are correct. Automated pay schedules cannot be run manually, so pause the automation first. (Creating a New Pay Run)
- Un-applied deductions are added to the open pay run so they fall in the right pay period. (Pay run deductions)
- The negative leave balance setting matches your leave policy. (How to Prevent Negative Leave Balances within Pay Runs)
- Super (from 1 July 2026, Payday Super): review pay categories that pay super and apply the Exclude from qualifying earnings setting where needed. Check any MCB overrides, and any employees under 18 on fortnightly or monthly pay cycles, who may need a manual qualifying earnings entry. (Payday Super (Qualifying Earnings & Annual MCB): What Admins Need to Do)
- Super fund verification: check the status of each employee and clear any Action Required items before the pay run. (Super fund verification (MVR) under Payday Super)
- Run a Qualifying Earnings Report to check qualifying earnings and super paid for the pay run. (Run a Qualifying Earnings Report)
Creating and checking the pay run
- Create the pay run, then add or remove employees as needed. (Process a pay run on Payroll classic)
- Work through pay run warnings and pay run tasks, such as child support or bank detail requests. (Pay Run Tasks)
- Recalculate the pay run after any changes, then check the variance and audit reports against the last pay run. (Recalculate the figures within a pay run on Payroll classic)
- If pay run approval is set up for the pay schedule, make sure the approver has approved the pay run before you finalise it. (Pay run approvals)
Finalise and pay
- Finalise the pay run from the Actions tab and check the preferences: HMRC or ATO submission, payslip publishing, employee notifications, report packs and pension. (Finalise a Pay Run)
- Lodge the finalised pay run with the ATO through Lodgement Options, and confirm the ATO has received it. (Lodge a finalised pay run to the ATO on Payroll classic)
- Download the ABA or BPAY payment file and send it to your bank before the cut-off. (Download payment files from a finalised pay run on Payroll classic)
- Check the pay run payments on the Pay Run Audit Report. (Pay Run Payments)
- Export the pay run and download the pay run journal for your accounting system. Exports do not include leave records or system-generated earnings lines. (Exporting a Pay Run)
If you need to correct a finalised pay run
- Unlock the pay run only if no automated super payments were made from it. Recalculate the pay run, then lodge an STP update event. (Unlock Pay Run)