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Payroll Software for Accountants
  • Publish: April 17, 2021
  • Author: StrongerTeams Editorial
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The Breakdown of the Best Payroll Software for Accountants

Accountants are an irreplaceable part of any business, no matter how big or small, as they are the ones who take care of your company’s financial well-being.

Their job is to keep track of your transactions, income, expenditures, profits and losses, and reports of your financial status, all of which play a crucial role in the success of your business.

The best payroll software solution is designed to facilitate the accountant’s job and automate the majority of the processes mentioned above. By utilizing one of the accounting payroll tools, your accounting team is going to save time spent on doing tedious tasks and minimize the chances of mistakes in calculations.

We know because we’ve been there. The founder of Stronger Teams, Nick Jordan, started his career as the 8th employee in a startup business that grew to 200 employees. Together with Gordana—our director of Operations—he grew ContentDistribution from 1 to 30 team members in 16 months.

During that time, we evaluated over a thousand, video interviewed hundreds of applicants, hired 50, and churned 20. Considering we had no formal HR experience, we soon recognized the need to use an HR-based software solution to keep track of all the invoices, payrolls, and other financial transactions.

We achieved our success through remote work culture and have personally researched and tested HR software solutions on the market. Our experience gives us accountability when it comes to comparing and establishing what makes the best HR software solution. We strive to provide you with all the necessary information in one place so you can make an informed decision.

Top 10 Accounting and Payroll Software Solutions

If you are in the market for payroll software for your accounting firm, we have done extensive research and compiled a list of ten tools that offer the best service:

  1. OnPay
  2. Wave Payroll
  3. Gusto
  4. QuickBooks
  5. Sure Payroll
  6. RUN Powered by ADP
  7. FreshBooks
  8. Patriot
  9. Paychex
  10. Wagepoint


OnPay is one of the best payroll software solutions for small businesses. One of its greatest strengths is that it integrates well with other accounting software options, such as Xero and QuickBooks, as well as most time tracking software solutions on the market.

It offers a variety of payroll services, such as calculating, filing, and paying payroll taxes, as well as payroll processing and direct deposits. It also automates benefits administration services, like health insurance deductions.

Comparatively, OnPay is quite affordable. It offers a base monthly fee with one of the lowest rates per employee. It will also customize its payroll services to the specific industry your business is in—at no extra cost!

Pros Cons
  • Affordable
  • Free account setup
  • Easy integration with time-tracking and accounting software
  • Fast
  • User-friendly
  • The mobile application is missing some functions
  • It offers only one paid plan

Wave Payroll

Wave Payroll is a free accounting payroll software with many useful features that other similar tools charge for. It connects to your bank account, tracks payments, expenses, and income, and offers invoicing and reporting services, among others.

Wave Payroll is mostly adapted for small businesses and freelancers as its features are not as comprehensive as in other software solutions. Considering all the benefits you get, it is still miles ahead of other free accounting payroll services out there.

Pros Cons
  • Free of charge
  • Simple-to-use interface
  • Time-saving
  • Lacks third-party integrations
  • Has limited features for larger businesses


Gusto is a well-rounded payroll software that offers accountants a full-service payroll plan. It handles all tax filings and has a great integration ability with other popular accounting software solutions.

While Gusto is a bit pricey, it’s definitely worth it, considering the time and money it will help you save in the long run. Gusto is accessible via Google Chrome or any mobile device.

Pros Cons
  • Wide variety of functions, even with the cheapest plan
  • Unlimited payroll runs in all states
  • Automatic local, state, and federal tax filing
  • Limited support (only daytime hours on workdays)


When deciding on which payroll software to opt for, it is crucial that you choose one that integrates with the software you’re already using. QuickBooks integrates with a wide variety of third-party apps and tools, such as Shopify, PayPal, TSheets, and SOS Inventory.

Besides integration services that eliminate manual data entries, QuickBooks offers complete payroll services—calculations, processing, and tax filing. These features save accountants precious time and provide much-needed accuracy.

Pros Cons
  • Affordable, considering the complex and adaptable features it offers
  • Suitable for businesses of all sizes
  • A limited number of users who can access the system
  • Sub-par online documentation

Sure Payroll

SurePayroll offers the best integration service, with all the payroll information sent to your accounting software, which saves you an enormous amount of time on manual entries. It also handles all payroll taxes—from initial reports to payment remittance.

If you are on a budget and require a quality software service, SurePayroll is considered to be one of the most affordable solutions out there.

Pros Cons
  • Great customer support service, available six days a week
  • Simple interface
  • Intuitive
  • Integration with accounting software costs extra

RUN Powered by ADP

RUN Powered by ADP offers a variety of useful services, such as great integration, tax filings, and payment remittance. It is the best possible solution for companies that have to take care of personnel matters because it provides both HR and payroll services. Every one of their plans offers at least a basic HR software solution feature.

Pros Cons
  • Easy integrations with third-party software solutions
  • Unlimited payroll runs
  • Easy-to-use interface
  • Customer service is slow to respond


FreshBooks is a payroll software solution adapted to small businesses, freelancers, and startups. It contains a limited but select range of features, so if you find yourself belonging to one of these categories, you will have all of your needs met at an affordable price.

Freshbooks started as invoicing software, but the original version has since been updated to cover double-entry accounting and offer a variety of integration options. It has been improving and adding features over the years, and it is now in the same range as Wave and similar software options.

Pros Cons
  • Easy to use
  • Excellent customer service
  • Affordable
  • The mobile app offers limited functionality (can’t access reports on the go)

Patriot Payroll

Patriot Payroll works best when coupled with Patriot Accounting. Apart from its great integration features, it also provides its users with the service of filing and depositing federal, state, and local payroll taxes.

Patriot Payroll processes year-end employee tax forms, such as W-2s and 1099s.

Pros Cons
  • Easy processing
  • Direct deposit
  • User-friendly
  • The direct deposit feature requires some adjustments and improvements


Paychex is a cloud-based software that, besides payroll, offers some basic HR services for companies that require that kind of support but don’t really need more complex HR features.

Every Paychex plan includes new-hire state reporting and automatic payroll tax filing. It also offers over 160 reporting options and lets you customize them according to your specific needs.

Pros Cons
  • Outstanding payroll service with tax filing
  • Great customer service
  • An extensive list of reports
  • Adapted to businesses with a maximum of ten employees


Wagepoint is an online payroll software that includes tax filings, direct deposit, and reports for the end of the year, all combined in one easy-to-use software. It is mostly recommended for small businesses and startups.

Pros Cons
  • Friendly customer support service
  • Simple and easy payroll service
  • Some functionalities need improving, like integration with other software solutions

What Features Should You Look For in Payroll Software for Accountants?

When deciding on payroll software solutions for accountants, consider some features mandatory:

  1. Integration with your existing accounting software. This feature allows you to integrate the data from the accounting software you are already using into the new payroll software solution. That way, the new software can use the data about leaves, entitlements, and payslip records and include it in future calculations
  2. Salary depositing. A great software solution for accountants will have the option of depositing the salaries directly into the employees’ accounts. This option will save you the bother of writing checks and printing slips, and you’ll avoid the expenses of preparing payrolls and reduce the costs of payment charges from banks
  3. Tax management. We all know that any irregularities in calculating taxes will be followed by severe penalties. It is one of the tedious jobs that fall onto the accountants’ shoulders. The right kind of payroll software for accountants will have the option of automatic tax calculations, which will leave no room for payroll mistakes
  4. Customization. As your company grows and expands, it is crucial you have payment software that you can adapt to the specific needs of your budding business. Make sure you can customize the components for calculating payments, such as penalties, leave entitlements, and compensation slabs

What Are the Benefits of Using Accountant Payroll Software?

We have presented the best software solutions for you to consider and the features you should be on the lookout for. What are the main benefits of choosing the right payroll software? Here is the list of the most significant ones:

  1. A higher level of accuracy. All of the automated features these software solutions provide will ensure you never have to question the accuracy of tax calculations, payments, and the overall financial state of your business
  2. Greater savings. When your accounting and payroll software function as one, you will save many hours of manual work as a result. The information you need is exported from one software to the other, so you don’t have to waste time on data entry, and you can shift your focus to other aspects of your business
  3. Additional HR services. Many software solutions for accountants have built-in HR software that provides some essential features for your HR department. Thanks to that, you can make sure your work processes run smoothly with all of the HR and payroll services in one place
  4. The practicality of the payment options. Most payroll software solutions for accountants offer different payment options—credit cards, direct deposits, mobile wallets, etc. All payments are resolved without the need to switch to another software, which can be confusing and time-consuming
  5. Free trials. They can help you decide which solution suits your needs best. Almost all of the payroll software solutions for accountants offer a free trial so you can test them out before committing to the right one

What To Consider Before You Decide on a Payroll Software for Accountants?

Here are some additional factors you need to have in mind before you start your quest for the best payroll software solution for accounting:

  1. What do I need from accounting software? The business you are in should determine the exact features to look for because not all software solutions offer the same. For example, if you are a service company, an important feature for you would be advanced project-management tools
  2. Should I choose free or paid accounting software? You have to consider the complexity of your business and then decide how refined you need the software to be. Free software solutions are a great option for smaller businesses because such tools usually offer a primary set of basic features that cover most of their needs. While free software can be good for your budget, it may also put you at some risk because of the diminished security. Paid software tools typically include advanced security and back-up systems in their plans
  3. Do I need bookkeeping or accounting software? Be careful not to confuse the two. It may seem that the bookkeeping software is all you need when you own a small business, but it only offers a limited amount of options. If you opt for accounting software, you will enjoy a larger number of features, like creating reports and invoicing
  4. Can I access my data from wherever I am? It is important to consider cloud-based software that allows you to access all the data without a hassle. You don’t have to be chained to your office anymore to be able to run a business—you should take full advantage of that with the right tool at your fingertips
  5. What are the user reviews like? It is always a good choice to check the reviews of other users when deciding on any product, and payroll software for accountants shouldn’t be an exception. That way, you can get an honest and agenda-free opinion from people who have direct experience with the software, as well as get some inside information about features

How To Negotiate the Price of Payroll Software for Accountants

Most of the software solutions offer plans depending on your requirements, but they also customize their prices if you have any special demands. The important thing to have in mind is that you can always negotiate the price with the vendor.

This can sometimes be challenging since the vendors are often more tech-savvy than you and have a lot of experience. We offer some tips for leveling out the playing field and getting everything you need at an affordable price.

When talking about the price and closing the deal with the vendor, always make sure to:

  • Ask about all the additional features you might need, and make sure there will be no previously unrevealed and unforeseen costs after you make the purchase
  • Get a copy of the contract

We all know how hard it can be to keep up with the challenges of business expansion. The need to adapt to new inventions that will facilitate our work life is always present. That includes spending too much time on multiple websites to find a solution that will cover all your specific needs. We took the time to research and answer your questions in one place.

For additional software solutions, you can check out our other reviews:

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