Payroll & HR Software
Top 10 Best Payroll Services for Australian Businesses in 2025
A clear comparison of the most reliable payroll platforms for STP Phase 2, superannuation, compliance and seamless employee payments.
Choosing the right payroll software is essential for Australian businesses managing STP Phase 2, super payments, award rates, and growing staff numbers. The right system helps prevent ATO errors, avoids late super penalties, and streamlines pay runs — whether you manage it in-house or outsource to a BAS agent like RJ Partnering.
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We implement payroll, STP Phase 2, super, BAS and bookkeeping for Australian SMEs.
1) Xero Payroll
Best for: Most Australian SMEs
- Complete STP Phase 2 compliance
- Automatic super contributions via Beam
- Timesheets, leave, pay templates and employee self-service
- Perfect for businesses already using Xero for accounting
Why choose it: Reliable, easy to learn and integrates with almost every add-on in Australia.
2) Employment Hero Payroll (KeyPay)
Best for: Award interpretation & shift-based staff
- Automated award rate calculations
- Roster, time & attendance built in
- Great for retail, hospitality, trades & franchise groups
Used widely by HR teams needing deeper automation than standard payroll platforms.
3) QuickBooks Payroll (Australia)
Best for: Small teams needing simple payroll + accounting together
- STP Phase 2 compliant
- Strong integration with QuickBooks Accounting
- Mobile approvals and flexible pay runs
Pair with our Payroll Processing Services for full BAS + bookkeeping support.
4) Square Payroll
Best for: Hospitality, retail & POS-heavy environments
- Integrated with Square POS for tips, commissions & shift hours
- Supports both employees and contractors
- STP + automatic super
5) MYOB Payroll
Best for: Businesses that prefer MYOB for accounting
- STP Phase 2 ready
- Employee portal, timesheets & leave
- Works well for accountants & larger established firms
6) CloudPayroll
Best for: Businesses wanting simple, stable payroll
- STP2 + superannuation automation
- Easy for owners and admin teams
- Excellent for micro to medium-sized businesses
7) Payroller
Best for: Sole traders & small employers
- ATO-approved and STP Phase 2 compliant
- Very low-cost option
- Simple interface + mobile app
8) Ascender / Frontier Software
Best for: Medium to large organisations
- Enterprise-grade payroll & HRIS
- Award interpretation + complex workforce management
- Ideal for companies with 100+ staff
9) Deputy + Payroll Add-ons
Best for: Shift-based industries using Deputy for rostering
- Timesheets sync directly into payroll platforms (Xero, EH, MYOB)
- Award interpretation based on rosters
- Ideal for hospitality, retail & construction
10) FoundU
Best for: Fast-growing businesses with complex compliance
- End-to-end HR, onboarding, rostering & payroll
- STP Phase 2 + super automation
- Ideal for multi-site operations
How to Choose the Right Payroll Provider
- STP Phase 2: Ensure full compliance to avoid ATO penalties.
- Super automation: Beam, Auto Super, or direct clearing-house integration.
- Award interpretation: Critical for retail, construction, hospitality & trades.
- Integrations: Must work smoothly with Xero, job costing or POS.
- Cost: Check for per-employee or per-pay-run fees.
Explore our Payroll Setup & Processing Services and Bookkeeping Services for end-to-end support.
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Book nowPayroll Services FAQs
What is the easiest payroll system for Australian small businesses?
Xero Payroll and QuickBooks Payroll AU are both simple to use, ATO compliant and suitable for most small businesses.
Can I run payroll myself?
Yes — platforms like Payroller and CloudPayroll are beginner-friendly. If you prefer, RJ Partnering can manage payroll, STP and BAS for you.
What’s the difference between payroll and HR software?
Payroll covers wages, STP, super and compliance. HR software adds onboarding, performance, policies, rostering and people management.
Does RJ Partnering offer payroll support?
Yes — we handle payroll processing, onboarding, STP Phase 2, superannuation, BAS and bookkeeping for Australian SMEs.