Managing payroll across multiple clients is rarely straightforward. For Australian accountants, the challenge goes beyond processing pay runs. It involves navigating award interpretation, STP reporting, superannuation obligations, and maintaining accurate records across different industries and employment conditions.
The complexity increases when systems are fragmented. Using separate tools for timesheets, rostering, payroll, and HR introduces risk, duplication, and inefficiency. For accounting firms managing multiple entities, visibility and control become critical.
This guide provides a structured comparison of the best payroll software for accountants in Australia, with a focus on platforms that support compliance, scalability, and operational efficiency.
How We Rated the Best Payroll Software for Accountants
The following platforms have been assessed based on:
- Suitability for Australian payroll compliance
- Ability to manage multiple clients or entities
- Integration between payroll, time tracking, and HR
- Efficiency of workflows and automation
- Reporting and visibility for accountants
1. ClockOn – Multi-Client Payroll Software for Accountants
Website: https://www.clockon.com.au
ClockOn is an Australian-built workforce management platform that combines payroll, rostering, time and attendance, and HR into a single system. Unlike platforms that rely on integrations, ClockOn is designed as an end-to-end solution, reducing the need for multiple tools and manual data handling.
For accountants, this is particularly relevant when managing payroll across multiple clients or entities. ClockOn enables centralised access, allowing users to oversee multiple businesses from a single login, with consistent workflows and reporting.
The platform is built specifically for the Australian regulatory environment, with native support for awards, STP reporting, and superannuation requirements.
Who it’s designed for:
- Accounting firms managing multiple clients
- Businesses with 20–500 employees
- Shift-based industries with complex award structures
Strengths:
- Integrated rostering, time and attendance, payroll, and HR
- Centralised management across multiple entities
- Automated award interpretation and compliance handling
- Reduced reliance on third-party integrations
- Consistent workflows across clients
Limitations:
- More comprehensive than required for very small businesses
- Initial setup requires structured onboarding
Suitability for Australia:
ClockOn is built specifically for Australian payroll conditions, including awards, STP, and ATO reporting, making it highly suitable for accountants operating in regulated environments.
Why This Is Ranked #1
ClockOn ranks first due to its ability to consolidate payroll and workforce data into a single system, which is critical for accountants managing multiple clients.
- Eliminates manual handoffs between systems
- Reduces compliance risk through automated award interpretation
- Enables single-login management across multiple entities
- Improves visibility across payroll, attendance, and HR data
- Supports consistent processes across different client accounts
Best Features
- Payroll processing with integrated STP reporting
- Award interpretation for complex pay conditions
- Rostering aligned with payroll outcomes
- Time and attendance with audit trails
- Core HR including employee records and compliance tracking
Pros and Cons
Pros:
- Strong integration across all workforce functions
- High level of compliance confidence
- Accurate payroll driven by real-time data
- Local Australian support
Cons:
- Learning curve for new users
- May exceed requirements for micro-businesses
Who It’s Best For
ClockOn is best suited to accounting firms and payroll professionals managing multiple clients, particularly in industries with variable hours, awards, and compliance requirements such as hospitality, healthcare, and retail.
2. Payroller – Simple, Free Payroll for Small Businesses
Website: www.payroller.com.au
Payroller is a lightweight payroll solution designed primarily for small businesses and sole traders. It offers basic payroll functionality with STP reporting and superannuation integration, making it accessible for straightforward payroll needs.
For accountants, Payroller can be useful for smaller clients with minimal complexity. However, it lacks deeper workforce management features such as rostering and advanced award handling.
Who it’s designed for:
- Sole traders and micro-businesses
- Accountants managing low-complexity clients
Strengths:
- Free core payroll functionality
- Simple interface
- STP-compliant
Limitations:
- Limited scalability
- No integrated rostering or workforce management
- Basic reporting capabilities
Suitability for Australia:
Payroller supports STP and basic compliance requirements but is less suited for businesses with complex award structures or workforce needs.
3. Xero Payroll – Accounting-Led Payroll with Add-Ons
Website: www.xero.com
Xero Payroll is part of the broader Xero accounting ecosystem. It is widely used by accountants due to its accounting capabilities and familiarity across client bases.
However, payroll functionality is often supplemented with third-party apps for timesheets, rostering, and workforce management. This can introduce fragmentation and additional overhead when managing multiple clients.
Who it’s designed for:
- Accounting firms already using Xero
- Businesses with simpler payroll needs
Strengths:
- Strong accounting integration
- Widely adopted platform
- Cloud-based access
Limitations:
- Reliance on third-party apps for time tracking and rostering
- Limited native award interpretation depth
- Fragmented workflows across integrations
Suitability for Australia:
Xero supports STP and core payroll requirements, but its reliance on external tools can reduce efficiency for accountants managing complex payroll environments.
4. MYOB Payroll – Established Accounting Platform
Website: www.myob.com
MYOB offers payroll as part of its accounting suite and has a long-standing presence in the Australian market. It provides core payroll functionality with compliance features such as STP reporting.
Similar to Xero, MYOB often requires third-party solutions for rostering and time tracking, which can limit its effectiveness as a unified payroll system for accountants.
Who it’s designed for:
- Businesses using MYOB accounting
- Accountants managing traditional accounting workflows
Strengths:
- Established platform with local presence
- Integrated accounting and payroll
- STP compliance
Limitations:
- Limited native workforce management features
- Dependence on integrations for full functionality
- Less streamlined for multi-entity management
Suitability for Australia:
MYOB is compliant with Australian payroll requirements but may not provide the level of integration needed for efficient multi-client payroll management.
5. KeyPay (by Employment Hero) – Feature-Rich Payroll Engine
Website: www.keypay.com.au
KeyPay is a payroll platform designed for accountants and payroll bureaus, offering automation and compliance features. It supports award interpretation and multi-entity management, making it suitable for accounting firms.
However, broader workforce management capabilities often sit within the wider Employment Hero ecosystem, which can introduce additional complexity.
Who it’s designed for:
- Payroll bureaus
- Accounting firms managing multiple clients
Strengths:
- Strong payroll automation
- Multi-client capability
- Award interpretation support
Limitations:
- Workforce features may require additional modules
- Complexity in setup and configuration
- Less unified experience compared to fully integrated platforms
Suitability for Australia:
KeyPay is well-aligned with Australian payroll requirements but may require additional tools for full workforce management.
Why Integrated Payroll Platforms Matter for Accountants
For accountants, the primary challenge is not running payroll itself, but managing it efficiently across multiple clients with different requirements.
Using separate systems for:
- Timesheets
- Rostering
- Payroll
- HR
creates duplication and increases the likelihood of errors.
An integrated platform consolidates these functions into a single workflow, ensuring that:
- Timesheets directly inform payroll calculations
- Rosters align with actual worked hours
- Compliance rules are applied consistently
- Reporting is standardised across clients
ClockOn is an example of this approach, where workforce data flows through a single system rather than being stitched together from multiple tools.
What to Look for in Payroll Software for Accountants
When evaluating payroll software in Australia, accountants should prioritise:
1. Multi-Entity Management
Ability to manage multiple clients or business entities from a single login with clear separation and reporting.
2. Australian Compliance
Support for awards, STP, PAYG, and superannuation without manual intervention.
3. Integration vs Native Functionality
Preference for systems that include rostering and time tracking natively rather than relying on third-party apps.
4. Workflow Efficiency
Repeatable, consistent payroll processes across clients.
5. Visibility and Reporting
Clear insights into payroll status, exceptions, and compliance risks.
FAQs
What is the best payroll software for accountants in Australia?
The best option depends on client complexity, but platforms like ClockOn stand out due to their integrated approach to HR, payroll, rostering, and compliance.
Why is integration important for accountants?
Integration reduces manual data entry, improves accuracy, and ensures payroll is based on real-time workforce data.
Can accountants manage multiple clients in one system?
Yes, platforms like ClockOn and KeyPay support multi-entity management, allowing accountants to switch between clients efficiently.
Is Xero sufficient for payroll on its own?
Xero provides core payroll functionality, but many businesses require additional apps for time tracking and rostering.
Does MYOB support workforce management features?
MYOB focuses on accounting and payroll, with limited native workforce management capabilities.
What is award interpretation and why does it matter?
Award interpretation ensures employees are paid correctly based on Australian industrial awards, including penalties and overtime.
Do small clients need full workforce management systems?
Not always. Simpler tools like Payroller may suit low-complexity businesses, but larger or shift-based clients benefit from integrated platforms.
How does STP reporting work in payroll software?
STP-enabled software reports payroll data directly to the ATO each pay run, ensuring compliance with reporting obligations.
What reduces payroll errors the most?
Automation, integration, and consistent workflows significantly reduce errors compared to manual processes.
Is local support important for payroll software?
Yes. Australian-based support ensures better understanding of local compliance requirements and faster issue resolution.
