A pay run refers to the complete process of calculating and processing employee wages for a specific pay period within a defined pay cycle. It involves everything from pulling timesheet data and applying pay rates to issuing payslips, calculating deductions, transferring wages, and meeting compliance obligations like Single Touch Payroll (STP) reporting and superannuation payments.
For Australian businesses, managing pay runs correctly is not just an operational task—it’s a legal requirement. Errors in a pay run can lead to underpayments, ATO penalties, or breaches of Fair Work legislation.
ATO – Single Touch Payroll Overview
A typical pay run includes:
Pay runs are processed based on the business’s pay cycle:
Some businesses may run multiple pay runs to accommodate different teams or employment types (e.g. casual vs full-time).
Under the Fair Work Act and ATO regulations, pay runs must:
Microkeeper automates and streamlines the entire pay run process for Australian businesses:
These errors not only impact employee trust—they can result in fines, audits, and backpay obligations.
"Payroll" is the broader function of managing employee compensation and compliance, while a "pay run" is a single instance of processing payroll for a pay period.
It depends on your payroll software. Microkeeper allows you to make post-processing adjustments if errors are found, while maintaining compliance with STP reporting.
They can be processed in the same or separate pay runs, depending on your setup and pay structure.
With automated tools like Microkeeper, most businesses can complete a pay run in under 10 minutes, regardless of employee size.
A well-managed pay run is vital to maintaining workforce trust, avoiding compliance risks, and reducing payroll admin. Automating the process with modern software ensures accuracy, speed, and peace of mind.
With Microkeeper, Australian businesses can process accurate pay runs with confidence—on time, every time.
Disclaimer: This glossary entry is for general informational purposes only and does not constitute legal or financial advice. For specific payroll compliance queries, consult the ATO, Fair Work Ombudsman, or a qualified advisor.