Choosing the best payroll software in Australia is not just about price. It is about finding a system that handles compliance, reduces admin, and fits how your business actually operates.

For some businesses, payroll sits inside accounting software. For others, payroll is part of a broader workforce system that includes rostering, timesheets, leave, and HR.

  See also: Best Payroll Software for Accountants & Bookkeepers  

For over two decades, we’ve been working with Australian businesses of all shapes and sizes to help them find payroll software solutions that work for them. So, we’ve put together a short guide to help you choose the right software for your business.

Below we compare some of the most commonly used payroll software options in Australia and explain which type of business each one suits best. 

Quick Comparison: Payroll Software Australia

What Makes Payroll Software “Best” in Australia?

Payroll in Australia is complex because of:

1. Modern Awards and Enterprise Agreements
2. Superannuation obligations
3. PAYG withholding
4. Single Touch Payroll (STP) reporting

The best payroll software is not the one with the most features. It is the one that reduces manual decisions and ensures payroll runs consistently every time.

Look for:

• Automated tax and super calculations
• STP-enabled reporting to the ATO
• Accurate record keeping aligned with Fair Work requirements
• Clear payroll workflows from timesheet to pay run

Australian employers must keep payroll records for 7 years, and those records must be accurate and not misleading. That makes system reliability critical, not optional.

Top Payroll Software Options in Australia

ClockOn

Best for: Businesses that want payroll connected to rostering, attendance, and HR

ClockOn is designed as a complete workforce management system, not just a payroll tool. It connects planned hours, actual hours, and payroll processing in a single workflow.

Key strengths

• Payroll, rostering, and timesheets in one system
• STP reporting built into the payroll process
• Automated award interpretation and pay conditions
• Real-time visibility of worked vs planned hours

Where it stands out

ClockOn is particularly strong for businesses with shift workers, multiple roles, or award complexity. Instead of managing payroll separately from operations, it brings everything into one system.

Consider if

You want more than just basic payroll and need operational control over labour, compliance, and workforce data.

Xero Payroll

Best for: Small businesses already using Xero accounting

Xero Payroll integrates directly with Xero’s accounting platform, making it a convenient option for businesses wanting everything in one financial system.

Key strengths

• Seamless accounting integration
• Simple payroll setup for small teams
• Native employee self-service and timesheets

Limitations

While Xero handles payroll well for many small businesses, some businesses require additional tools when workforce management becomes more complex.

MYOB Payroll

Best for: Businesses already operating within MYOB

MYOB offers payroll functionality within its broader accounting ecosystem.

Key strengths

• Familiar workflows for existing MYOB users
• Payroll setup aligned with accounting processes
• Employee onboarding and payroll configuration tools

Limitations

Primarily suited to accounting-led workflows rather than operational workforce management.

ADP

Best for: Larger businesses or those considering managed payroll

ADP provides payroll software alongside managed payroll services.

Key strengths

• Scalable payroll and HR capabilities
• Suitable for complex organisational structures
• Option for outsourced payroll support

Limitations

Often more complex and service-oriented than what smaller businesses require.

Why Must Payroll Records Be Kept?

There are several reasons why complete payroll records need to be kept and organised for a minimum of 7 years. If you neglect to keep records of your employees or you’re found to be updating records with false information, there could be severe legal consequences for you and your business. 

• For audit purposes. If your business is audited, you need to have comprehensive records of your employees to prove you have been paying them correctly. 
• For the employees themselves. Whether they are currently employed with your business or a former employee, people who have worked for you may require their records in the future. You need to have retained payslips, contributions, a record of hours worked, leave entitlements, end of employment documents, and general information such as names, an address, phone number, tax file number, and other pieces o essential information. 
• For your tax and ATO obligations The ATO requires all Australian businesses to report employees' payroll information each time you pay them. This is known as Single Touch Payroll (STP). To correctly report your payroll data to the ATO, you need to use ATO-approved payroll software and keep detailed records of your employees’ pay history. 
  
  

Why Is Payroll Software Important For Small Businesses? 

Payroll software takes a lot of guesswork, time, and human error out of payroll processes. Here are a few reasons why payroll software is such an essential addition to your business. 

• Get all your information in one place. Payroll software makes it simple to access information in one accessible place. You can find anything you need at the click of a button. Additionally, you’ll be better able to keep long-term records of employees and payments.
• Remain 100% compliant. Payroll software keeps track of current award rates, leave accruals, and ATO reporting. You can rest assured knowing that your payroll obligations are streamlined and automated. 
• Save yourself time. Instead of spending hours on payroll each pay period, leave payslip generation and other payroll tasks to your payroll software. Spend that extra time growing your business and focusing on the things that need your attention. 
• Access comprehensive reporting. Whether you need information on leave accruals, bonuses given, or financial information for BAS and PAYG lodgments, your payroll software will provide you with detailed, easy-to-understand reports with the click of a button. 
• Ensure employees are paid correctly. With payroll software, you can generate payslips, calculate salaries, calculate tax deductions and super contributions, and even complete more complex functions such as bonus payments. 
  
  

How To Choose The Right Payroll Software

Now you know why you should get payroll software, the next question is how to choose your business’s provider. Here are a few tips for picking the right software. 

• Look for something easy to use. The last thing you want is to buy payroll software and then not understand how to use it. Make sure you’re investing in software that is intuitive, clear, and simple. Comprehensive online help resources and Australian-based support teams are also highly desirable features to look for.
• Avoid the ‘one-size-fits-all’ approach. Your business is unique, so your payroll needs will be unique too. Look for payroll software that allows you to choose which features to include in your package and which to leave out. At ClockOn, we work with our clients to figure out what they need from their payroll software, and we avoid adding extra features we know they won’t use. 
• Where do you see your business going? One of the most important features of high-quality payroll software is scalability. Whether you’re growing your business rapidly, you’re looking to maintain consistency, or you’d like to scale things back, you need to invest in software that can cater to your needs. 
• Choose payroll software that fits your budget. Cutting-edge, innovative payroll software should be accessible to businesses of all sizes. That’s why we offer affordable monthly plans tailored to the number of employees you have. 
• Pick a provider than understands Australian businesses. Unlike some of the bigger, international names in payroll software, ClockOn is Aussie-owned and operated. We understand Australian companies’ unique needs, so we’ve developed software and an app that specialise in making the lives of Aussie business owners and employees easier. 
  
  

The Best Payroll Software Providers In Australia

When selecting payroll software for your business, you’ll want to make sure you’re getting the best service possible. We’ve listed a few of the best providers in Australia so you can pick the right fit for your business. 

• Xero. Xero is primarily an accounting software platform for small and medium-sized businesses but in recent years they have expanded their functionality and have gained a large market share of the Australian Payroll market. It’s particularly popular for those customers that already use the accounting module; Xero accounting subscribers can simply bolt-on a payroll module to their package. It is beautifully designed software and integrates well with other well-known software.
  
  CON: A common issue many find with Xero is its difficult to track time effectively. This results in many Xero payroll users needing a 3rd-party timesheet software that integrates with Xero to track their staffs start- break and end times.
  
  See: Why Many Australian Businesses Move Beyond Accounting Payroll
  
  
• ADP Workforce Now. This is somewhat of a hybrid between payroll software and an outsourced payroll service. It is a popular option but because of the human involvement, it comes at a higher cost than standalone payroll software.
  
  
• MYOB. This software is very flexible to fit with various industries and sectors, and it’s scalable for small to medium businesses. Like Xero, MYOB is also primarily accounting software but makes available a payroll module to its accounting subscribers.
  
  
• ClockOn. Originally known for its powerful, advanced features, ClockOn has pivoted into more user-friendly software catering for small and medium sized businesses. If you’re looking for value, look no further than ClockOn – we offer free payroll software for businesses with less than 20 employees. Businesses with more than 20 employees are charged per employee at a rate of just $2.25  per employee, per month.
  
  

Why Many Australian Businesses Move Beyond Accounting Payroll

Accounting-led payroll works well early on.

But as businesses grow, gaps start to appear:

• Timesheets live outside payroll
• Rosters are disconnected from actual hours
• Manual checks increase risk
• Compliance becomes harder to manage

This is where integrated systems like ClockOn become more valuable. Instead of stitching together multiple tools, businesses can manage payroll, workforce, and compliance in one place.

Why Choose ClockOn For Payroll Software? 

ClockOn is quickly becoming one of Australia’s favourite payroll software providers, and it’s not hard to see why. 

• Easily accessible by everyone in the business. ClockOn’s payroll software is fantastic for both staff and management. Management can see wages, super, taxes, and leave requests all in one place, and employees can use ClockOn GO to check rosters, receive payslips, lodge leave, and track their hours. 
• Integrations and Exports. For even greater business efficiency, you can connect your ClockOn system with other popular software such as MYOB, Xero and any Superfund that supports the SAF file format.
• Access a range of other services. In addition to our payroll software, ClockOn also has rostering and attendance modules. For a more hands-off option you can engage our outsourced payroll team. They will ensure your payroll is processed accurately and in accordance with Australian tax and superannuation legislation.
• We care about your business. At ClockOn, we value each of our clients and their businesses. We’re here to help Australian businesses grow and thrive, and we offer streamlined payroll solutions to help make that happen. 
  
  

If You’re Looking For Payroll Software For Your Business, Contact ClockOn

With over 20 years of industry experience, the team at ClockOn have found the best, most efficient methods of simplifying your payroll systems. We’re committed to making payroll easier for business owners, so we’ve come up with software to save you time on workforce management and payroll-related tasks. If you’re interested in learning more about our software or to simply find out what ClockOn can do for you, don’t hesitate to contact us today. 

See if ClockOn is right for your business