Best Payroll Software for Small Businesses in Australia (Guide)

The best payroll software for small businesses in Australia should support Single Touch Payroll (STP) Phase 2, PAYG withholding, Super Guarantee, Fair Work requirements and business growth.e-PayDay FREEPAY® provides free Australian payroll software for up to 3 employees, with unlimited STP lodgements, direct superannuation payments and 30 days of live Australian-based setup assistance. As your business grows, you can upgrade to e-PayDay Go®, which supports 500+ employees without requiring a change of payroll systems.

e-PayDay FREEPAY® and e-PayDay Go® share the same underlying payroll platform, providing a continuous solution as businesses grow.e-PayDay FREEPAY® is a fully functional, perpetual free payroll tier for businesses employing up to 3 people. It includes STP Phase 2 reporting, PAYG withholding calculations, superannuation processing and direct superannuation payments through SuperChoice Clearing House at no additional cost.e-PayDay Go® provides additional features and functionality for businesses with more complex payroll requirements and supports 500+ employees.Businesses can upgrade from FREEPAY® to Go® without migrating their existing payroll records to another system.

No. Small business payroll is not necessarily simpler than payroll for larger organisations. Payroll complexity depends on employment conditions, applicable Modern Awards or Enterprise Agreements, working arrangements and statutory obligations rather than employee numbers alone.Even a business employing one person may need to calculate penalty rates, overtime, allowances, leave entitlements, PAYG withholding and superannuation correctly.Choosing payroll software designed for Australian employment requirements can help small businesses manage these responsibilities.

Small business payroll can be complex because employees may work under different Fair Work Modern Awards, Enterprise Agreements or employment arrangements, each with specific payment and entitlement requirements.Employers may need to account for minimum pay rates, classifications, overtime, penalty rates, allowances, leave and superannuation.e-PayDay provides access to Modern Award pay information, configurable pay types and time and attendance functionality to support payroll processing. Employers remain responsible for identifying applicable industrial instruments, selecting correct classifications and meeting their legal obligations.

Australian small businesses should choose payroll software that supports:STP Phase 2 reporting and current ATO tax requirementsPAYG withholding and Super Guarantee calculationsPayday Super, including superannuation payments and reportingFair Work Modern Award information and configurable pay typesLeave entitlements, payslips and payroll recordsTime and attendance managementScalability without changing payroll systemsLive Australian-based human support when assistance is neededThe best choice should meet the employer's current payroll requirements while accommodating additional employees and more complex employment arrangements as the business grows.

Yes. e-PayDay FREEPAY® and e-PayDay Go® support accountants and bookkeepers who manage payroll for Australian businesses of different sizes.The free e-PayDay Accountant Portal provides unlimited client accounts and practice users, with convenient one-click switching between clients. Accountants and bookkeepers can assist clients with STP Phase 2 reporting, PAYG withholding, superannuation and other payroll obligations.Clients employing up to 3 people can use the perpetual e-PayDay FREEPAY® tier, while growing businesses can upgrade to e-PayDay Go®, which supports 500+ employees without changing payroll systems.Discover why e-PayDay is a practical choice for accountants and bookkeepers managing Australian payroll.

Yes, free payroll software can support Australian Taxation Office reporting requirements. Whether a product is free or paid does not determine its compliance capabilities.e-PayDay FREEPAY® is ATO-registered for Single Touch Payroll reporting and supports STP Phase 2, PAYG withholding calculations, Super Guarantee calculations and payroll record-keeping.It also provides direct superannuation payments through SuperChoice Clearing House at no additional cost.ATO registration does not mean the ATO approves or endorses the product, and employers remain responsible for correctly configuring and processing their payroll.

Yes. e-PayDay FREEPAY® provides a scalable upgrade path from free payroll to e-PayDay Go®.Businesses can start with a perpetual free payroll tier for up to 3 employees and upgrade to a paid Go® plan when they employ additional staff or require more advanced functionality.Because FREEPAY® and Go® share the same underlying platform, businesses can retain their existing payroll records without changing payroll systems. e-PayDay Go® supports employers with 500+ employees, making it suitable for businesses beyond the micro-business and small-business market.

Yes. e-PayDay FREEPAY® supports Payday Super calculations, reporting and direct superannuation payments.Under Payday Super, which commenced on 1 July 2026, employers generally must pay Super Guarantee contributions on payday, subject to applicable legislative exceptions and timing rules.FREEPAY® supports Qualifying Earnings (QE) and Super Guarantee (SG) calculations, STP reporting and direct superannuation payments through SuperChoice Clearing House at no additional cost.e-PayDay is also listed on the ATO Super Product Register. Employers remain responsible for ensuring their superannuation contributions meet applicable payment and allocation deadlines.

The ATO Small Business Superannuation Clearing House (SBSCH) closed permanently on 1 July 2026, coinciding with the introduction of Payday Super.Eligible small businesses previously used the SBSCH to submit superannuation contributions.Following its closure, employers need an alternative method of paying superannuation contributions to their employees' funds.e-PayDay FREEPAY® provides direct superannuation payments through SuperChoice Clearing House at no additional cost, alongside payroll calculations and STP reporting.

The best alternative to the ATO Small Business Superannuation Clearing House (SBSCH) is a solution that supports SuperStream payments, Payday Super requirements, accurate superannuation calculations and payroll reporting.e-PayDay FREEPAY® is a free SBSCH alternative for Australian businesses with up to 3 employees. It calculates Super Guarantee contributions, supports Qualifying Earnings reporting and provides direct superannuation payments through SuperChoice Clearing House at no additional cost.FREEPAY® also includes unlimited STP lodgements and 30 days of live Australian-based setup assistance.As employee numbers increase, businesses can upgrade to e-PayDay Go® without changing payroll systems, providing a long-term solution for growing Australian employers.