When it comes to small businesses in Australia, there are quite a few choices when it comes to payroll systems. The type of payroll software you choose can have a huge impact on your business and employees. It’s important to carefully consider the needs and requirements of your business and employees so you can pick an effective and simple payroll system.
Here are the best out there!
BEST OVERALL Gusto
Gusto offers three thoughtful tiers for small to midsize companies that need payroll with a few helpings of human resources (HR) features, making it the best overall choice. Each plan includes full-service automated payroll that’s suitable for almost any business, depending on needs.Pros
- Affordable, but good value
- Unlimited payroll runs
- Paid time off (PTO) tracking available
- Full-service payroll available in all states
- Basic reports included at all tiers
Cons
- Next day direct deposit available only in the Complete and Concierge plans
- Dedicated support only for Concierge subscribers
Gusto is similar to other payroll software solutions in that it offers direct deposit or checks to pay your employees. It also tracks and files federal, state, and local taxes automatically. What sets Gusto apart from the other options is that it offers a better plan for each tier that you go up. Rather than removing direct deposit for the low-priced plan, Gusto increases the convenience of direct deposit the more expensive your plan. For example, direct deposit takes up to four days to clear for the lowest plan, but the high-tier plans get next-day direct deposit.
The Core plan from Gusto costs $39 per month, and $6 per employee per month, making it one of the most affordable choices for a full-service payroll plan. The Complete plan is also $39 per month, but the cost per employee is $12, and you’ll be able to offer next-day direct deposit. The Concierge plan is $149 per month and $12 per person and offers dedicated support and compliance alerts.
BEST REPORTING Paychex Flex
Paychex Flex offers more than 160 reports for you to get a clear look at wages, taxes, turnover, and more. Paychex is our best reporting option because it checks almost all the boxes for what you’d want in payroll software when it comes to reports and data. It also automatically files your payroll taxes, ensures compliance, and includes integrations with important programs you also use, such as accounting and benefits apps.Pros
- 24/7 support
- Easy to use
- HR add-on options
- Robust reporting feature
Cons
- Hidden fees for setup & EOY tax docs
- Mixed reviews from users regarding support
There’s a lot to like about Paychex. The payroll software makes it easy to set up and run payroll, it automates the submission of federal, state, and local payroll taxes, and it offers plenty of upgrade options, which you may need as your business grows. Still, the basic reporting you get from Paychex could be worth the monthly fee alone, giving it the edge in this category. Plus, you’ll be able to add any other data field you’d like, thanks to custom fields, which is rare for small business online payroll services.
While the Paychex Flex Essentials plan is $39 per month and $5 per employee, it’s difficult to say how much Paychex will cost you for the more comprehensive plans—Paychex Flex Select and Paychex Flex Pro—unless you go through the process of getting a custom quote.
One of the most important aspects of a good online payroll solution is whether it integrates with software you already use. Paychex does integrate with QuickBooks and Xero accounting software, plus many health insurance and benefits apps, time tracking and attendance software, and HR software.
RUNNER UPs
ELMO

ELMO offers an integrated payroll and HR system to help you manage all your employee-related tasks. This integrated platform aims to increase efficiency and reduce operations costs.
It allows the onboarding process to seamlessly flow into payroll. Thus, it eliminates the need for additional data entry or transfer. Besides, the system ensures that you effectively organize your timesheets and pay your employees on time.
Features
- Offers a secure and compliant-ready payroll
- Allows you to generate in-depth reports to help you make smart decisions
- Very easy to install and use
Xero

Xero offers an integrated payroll system with its accounting software. However, it comes with a full-fledged functionality of a payroll solution. It automatically keeps updating the amount pending to be paid, which you can view from your accounting solution.
It provides tools to track the number of hours worked by each individual and keep records of the number of leaves taken. Besides, it can be accessed from any device – desktop, mobile phones, and tablets. It syncs the information in real-time.
Features
- Has an intuitive and clean interface for the ease of use
- Makes it easy for employees to apply for leave or view their payslips
- The system is SuperStream compliant
MYOB

MYOB is one of the best payroll systems that is best suited for small to medium-sized companies. It is designed locally to serve the local businesses with the ATO compliant.
They offer a single touch payroll that makes the entire process of paying staff super quick. Using the system, you can easily generate detailed reports on all your employee details, the payments made, time tracking and attendance records, and much more.
Features
- Has an active and reliable support team, available 7 days a week
- Offers a rich and easy-to-use interface
- Offers high security to protect your business data
Payroll Metrics

Payroll Metrics offers an enterprise-level payroll solution that comes integrated with workforce management software. It is an all-in-one solution that enables you to automate your business processes and achieve complete efficiency.
This modern, reliable payroll software in Australia empowers employees and managers with self-service. Employees can have access to view their payslips, request leaves, and more.
In fact, it can even create organization charts and workflow hierarchies.
Features
- Compatible with all devices with a web browser
- Generates smart reports for detailed insights
- Can import employee updates from your HRIS software
QuickBooks Online

QuickBooks Online is a sophisticated platform that offers an integrated payroll system within its accounting software.
The system automates the entire process of accurately calculating the payroll and processing the payment on time. It stays compliant with all the requirements of ATO. Besides, it even offers a single touch payroll solution.
It is quite simple to use. Login to QuickBooks online, enter your business and employee details, and add pay run information. That’s it.
Features
- Enables employees to update their own personal details
- Offers excellent customer support for any technical issues
- The system is highly scalable and secure
Smart Payroll

Smart Payroll is a cloud-based payroll system that is quite popular in Australia. They bring their 10 years of payroll expertise into this solution.
The system keeps you updated about the correct tax slabs so that no mistake is made. It allows you to automate the process of directly depositing payments into the employee’s account.
Besides, the system is fully backed up so that you don’t have to stay worried about losing the data.
Features
- Generates detailed reports as per your business needs
- Enables employee self-service through its MyPay app
- Offers full support to all its customers
KeyPay

KeyPay is an award-winning payroll software that offers a robust set of functionalities. This cloud-based solution automates payroll processes, saving you extra time to focus on more important tasks.
With its self-service app WorkZone, both employers and employees can manage their own information. Using the app or an online portal, they can request for leave, update their timesheets, track their reimbursement status, and more.
Most importantly, it streamlines the complete payroll process and provides real-time insights into the operating cost of your business.
Features
- Seamlessly integrates with third-party applications
- Suitable for all size of businesses
- Has a rich and intuitive dashboard for easy access
Sage

Sage is a powerful payroll software that can be used by all sizes of businesses. It streamlines and automates the payroll processes, including payslips and tax calculations.
The system is regularly updated to ensure that the businesses stay compliant with any changes in the payroll and pension legislation. This cloud-based solution aims to minimize payroll administration by offering flexible reporting options.
Features
- It is a safe, secure, and intuitive payroll solution
- Offers active support for immediate assistance
- Helps you stay single touch payroll (STP) compliant
Clockon

Clockon is one of the most popular attendance and payroll software in Australia. It aims to streamline and automate the process of tracking the number of hours worked and accurately calculating payrolls.
It is endorsed by ATO and stays compliant with single touch payroll. It can generate up to 250 different types of reports to give you a detailed insight into your business management. It also offers dedicated mobile apps to enable employees view their payslips, update timesheets and personal details, and more.
Features
- Easily integrates with third-party applications
- Can generate and share payslips via email as well as mobile
- Offers good customer support for any kind of assistance
ADP

ADP is your one-stop solution to all your payroll needs. It offers you a secure, cloud-based platform to allow you to access your information from anywhere, anytime. It gives you full visibility into your workforce information.
In fact, it allows employers and employees self-service to request/approve leaves, view payslips, and more. Furthermore, it can seamlessly integrate with HR systems and ERPs for smooth operations.
Features
- Can generate over 100 standards reports for detailed insights
- Stays in compliant with ATO and STP regulations
- It is quite easy to use with its rich interface
Affinity

Affinitiy is another best payroll system that automates and removes errors from payroll processing. It is a cost-effective solution that is quite simple to use and reduces extra effort.
It offers robust reporting tools that provide you with great insights to help you make smart and informed business decisions. Some of its other functionalities include time management, self-service and workflow, remuneration packaging, leave management, and more.
Features
- Automated data sensitivity to protect it from new starters and terminations
- Gives you immediate visibility over resource allocation
- Integrates with third-party systems
Conclusion
Payroll Systems is one of the most important things to any business especially for small businesses. There is a misconception in the world of technology is that only large companies use software in the management of their payroll. This is not so. There are different types of payroll systems for small businesses nowadays and it is becoming easier than ever before to find the right solution for your business.