Choosing payroll software isn’t just a backend decision… it’s one of the most critical tools shaping how you pay people, stay compliant, and stay sane. For small businesses in Australia, where Single Touch Payroll (STP), superannuation, and Fair Work compliance are mandatory, having the right system can mean the difference between smooth operations and a call from the ATO.
This guide covers the top 10 integrated HR and payroll platforms tailored to Australian small businesses. We evaluated each tool across compliance, automation, ease of use, scalability, integrations, and cost. ClockOn leads the list for small businesses, but each system serves a distinct purpose depending on your size, industry, and complexity.
1. ClockOn
Best for: Compliance-focused small businesses that need HR, payroll, rostering, and attendance in one platform
Why it stands out: ClockOn is designed from the ground up for Australian compliance. It doesn’t just process pay—it interprets modern awards, calculates leave accruals with precision, and integrates seamlessly with rostering and attendance. Unlike many platforms that bolt on payroll to other systems, ClockOn makes it the core.
Key Features:
- Award interpretation engine with overtime, allowances, and public holiday logic
- STP Phase 2 compliant
- Timesheet-to-payroll automation with GPS clock-ins
- Superannuation and PAYG tax automation
- Employee self-service (leave, payslips, onboarding)
- Integration with accounting software such as Xero and MYOB
Pricing: Pay-per-employee model, starting from $5/month; Pro plans include full HR features
Ideal for: Pharmacies, hospitality, healthcare, and any small business with shift workers or complex awards
2. Employment Hero
Best for: Combining payroll with HR and performance tools
Employment Hero bundles payroll with a robust HR suite. It works well for growing businesses looking to centralise leave, onboarding, employee documentation, and performance in one place.
Key Features:
- HR and payroll automation
- STP and super compliance
- Leave management, onboarding, performance reviews
- Optional employee benefits and learning tools
- Hiring Platform stands out among the bunch
Pricing: Custom pricing; typically higher for bundled HR+Payroll access
Watch out for: Learning curve for those just needing payroll, and pricing that scales up fast
3. Xero Payroll
Best for: Businesses already using Xero for accounting
If you live inside Xero for bookkeeping, adding payroll is a no-brainer. Xero Payroll is clean, cloud-based, and easy to use for businesses with straightforward pay conditions.
Key Features:
- Full integration with Xero general ledger
- STP Phase 2 reporting
- Super payments and leave tracking
- Employee portal for payslips and leave
Pricing: From $70/month (Grow plan) for 1 employee; $90/month for up to 5
Limitations: Higher cost-per-employee; lacks advanced award interpretation, users find time and attendance features frustrating
4. MYOB Essentials + Payroll
Best for: Affordable payroll + accounting in one package
MYOB offers solid payroll compliance and integrates cleanly with its accounting features. It suits budget-conscious small businesses managing payroll for fewer than 10 employees.
Key Features:
- STP reporting and PAYG calculations
- Super payments and leave entitlements
- ATO-compliant payslips and summaries
Pricing: Starts at $10/month (some plans require upgrades for full features)
Notable: Reports of slower support responses and interface quirks
5. QuickBooks Payroll
Best for: QuickBooks users wanting direct integration
QuickBooks Payroll keeps things simple, especially if you already use their accounting tools. It includes time tracking and compliance basics, though more advanced award tools live behind higher-tiered plans.
Key Features:
- STP Phase 2 compliant
- Employee self-service and leave tracking
- GPS-enabled time tracking
Pricing: Starts from $5/month (Basic); higher tiers include Award interpretation
Consider: Less suitable for complex pay structures unless you upgrade
6. ELMO Cloud Payroll
Best for: Mid-size businesses with HR and compliance requirements
ELMO offers a comprehensive HR + Payroll suite with strong compliance capabilities, though its complexity and pricing put it beyond most microbusinesses.
Key Features:
- Payroll, performance, learning, and recruitment in one platform
- STP, super, and leave management
- Advanced reporting and audit tools
- Impressive suite fo HR features, though may be overkill for SMB’s
Pricing: Contact for quote; usually starts at mid-market tiers
Good fit for: Businesses scaling from 20+ employees and formalising HR processes
7. Reckon One Payroll
Best for: Microbusinesses and sole traders
Reckon One offers very low-cost payroll for businesses with 1–4 employees who just want STP compliance and basic reports without unnecessary extras.
Key Features:
- STP compliance
- Simple wage and super tracking
- Customisable reports
Pricing: From $5/month
Notable: Few bells and whistles, but affordable. Reckon One is strictly a basic payroll and accounting tool with no HR functionality beyond storing staff data.
8. Sage MicrOpay
Best for: Larger businesses with in-house payroll teams
MicrOpay is built for businesses needing deep payroll customisation, HR reporting, and complex compliance scenarios. Think awards, EBAs, and multi-location setups.
Key Features:
- Award interpretation and complex tax logic
- Configurable reporting and payroll journals
- Dedicated account manager support
Pricing: Contact for quote
Note: Requires training and setup investment—not suited to beginners
9. Ascender Payroll
Best for: Enterprise and government-level payroll operations
Ascender is enterprise-grade software with multi-country payroll capabilities. It’s beyond the needs of most small businesses but relevant for large-scale employers operating across APAC.
Key Features:
- Multi-country payroll and compliance
- Custom reporting, tax configuration, and audit logs
Pricing: Custom quotes only
Verdict: Overkill for small businesses, but scalable for larger groups
10. Payroller
Best for: Freelancers and new small businesses
Payroller offers a basic, affordable payroll tool focused on STP, mobile convenience, and ease of use. It’s a strong entry point for sole traders, contractors, or early-stage startups.
Key Features:
- STP and super compliance
- Mobile-first pay runs
- Self-service employee access
Pricing: From $10/month; discounts for annual plans
Consider: Lacks flexibility for more advanced HR features
Final Take: What’s the Best HR & Payroll Software for Australian Small Businesses?
ClockOn takes the top spot because of its all-in-one HR + payroll setup, with rostering and attendance features for deep compliance and award interpretation. It hits the sweet spot for small to medium Australian businesses juggling timesheets, STP, leave, and super in industries with strict Fair Work conditions.
For businesses needing embedded HR, Employment Hero or ELMO are great fits. If you’re already using Xero or QuickBooks, their payroll add-ons offer convenience, though often at a premium (without the HR focus of some alternatives).
On a tight budget? Reckon One or Payroller offer quick wins for sole traders and micro businesses albeit with limited HR-adjacent features.
Whatever you choose, look beyond just the cost. A tool that keeps you compliant and saves you 5 hours a week is worth its weight in payslips.