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Best Payroll Software for Accountants

Written by:

Mark Stewart is the in-house Certified Public Accountant, an accomplished author and financial media specialist.

Reviewed by:

Daniel Eisner is a payroll specialist with over a decade of practical experience in senior accounting positions.

Best Payroll Software for Accountants

Best Payroll Software for Accountants

If you’re an accountant and plan to handle payroll for multiple clients, the payroll process can get complicated. Dealing with payroll is often complex and time-consuming, which is why many accountants turn to a professional payroll service or software. 

Payroll services or software can make it simple for you to handle your clients’ payroll needs.

But with so many payroll services and software in the market, how do you know which are the best services for accountants?  And which is the right choice for you? This review takes a closer look — putting ourselves in the shoes of an accountant — to help you determine which option is the right payroll service or software for your accounting business.

Best Payroll Software for Accountants



Paycom’s all-inclusive HR software services are more expensive, but they include tools and features that offer businesses an outstanding value.



Zenefits is an user-friendly and easy-to-use payroll software that comes at a cost-effective price tag.



If you’re looking a full-service human capital management (HCM) solution, then we recommend Paycor.

Thomson Reuters Accounting CS Payroll


As a software designed specifically for accountants, Thomson Reuters offers a number of rich features that make it easy to manage the payroll.

1. Paycom

Paycom is an industry-leading HR software service provider that supports nearly 34,000 companies daily, according to their website. 

Paycom offers businesses a large spread of HR and payroll services that aim to satisfy a wide variety of business types and needs. Within one software application, businesses will find tools to assist with talent acquisition, time and labor management, talent management, HR management, and, of course, payroll duties. 

Pricing and features

Paycom’s payroll service offers a suite of six tools that can take many tasks off your plate and allow you to focus on more pressing business matters. Paycom’s payroll tools include Beti, Paycom Pay, GL Concierge, Expense Management, Garnishment Administration, and Payroll Tax Management. 

Beti, for instance, aims to help employees process payroll on their own, guiding them through an automated process that notes errors and provides troubleshooting assistance when needed. Employees are responsible for confirming the accuracy of their payouts, reducing the work of HR teams. 

Paycom’s Payroll Tax Management tool provides automated payroll tax deductions and filings, handling federal, state, and local tax filings, including employee W-4 and I-9 forms, as well as W-2s and 1099s. 

Pros and Cons


  • All-in-one HR software solution
  • Extensive mobile app capabilities
  • Great customer support
  • User-friendly software design


  • Lack of transparent pricing
  • Limited integration options
  • Not as useful for smaller businesses that need fewer service

Our Verdict

Overall, we were pleased with our Paycom experience. The site is easy to use, information is readily available, and it doesn’t take long to request a meeting with a representative. 

Their customer service is rather weak, as they have no live chat support and no email addresses listed on their website. When we called to speak with a customer service phone representative, however, our call was answered quickly and politely. 

Paycom’s all-inclusive HR software services are more expensive than most competitors, but all of the included tools and features offer businesses an outstanding value– especially large businesses. Based on our thorough research, we feel confident recommending Paycom to business owners. 

2. Zenefits

Zenefits’ platform of HR business solutions was made specifically for small and mid-sized businesses, which often face challenges disproportionate to their size and resources. 

Zenefits’ mission is to “level the playing field for the other 99.7%”, meaning the smaller businesses that keep our economy running. The company provides “innovative and intuitive HR and payroll software and services purpose-built” for smaller companies.

Pricing and features

The Zenefits Essentials plan comes with a variety of features and benefits. The automated onboarding feature includes offer letter generation, background check support, and digital documents with electronic signature capabilities. There’s also an employee self-onboarding feature where employees can complete and submit their new hire paperwork. 

The Essentials plan also comes with time tracking and reporting features to help businesses manage their PTO policies. The scheduling feature allows management to create and edit shifts and it also integrates seamlessly with the Zenefits payroll system. There’s also a user-friendly mobile app for employers and employees to access information on the go.

The Zenefits Growth plan includes all of the features from the Essentials plan plus compensation and performance management benefits. The compensation management features include real-time comparison salary data that can be integrated into an organizational chart. You can also create custom salary benchmark reports.

With the performance management benefit, businesses can improve employee performance with user-friendly, easy to administer tools. A full suite of performance review templates are available as well as goal setting and tracking features.  

The Zenefits Zen plan includes all of the above plus employee engagement survey tools and an interactive social platform called the People Hub. The employee engagement tools allow clients to customize their own surveys or use pre-built templates. 

The reporting features allow results to be filtered by employee demographics and you can view answers on a question-by-question basis. Feedback is collected anonymously to help keep employee responses private and confidential. 

The Zenefits People Hub is a customizable company social feed where administrators and employees can post announcements. It has interactive features such as the ability to like posts and comment to ask questions. 

Pros and Cons


  • Essentials plan is a great value
  • Robust HR support included in all plans
  • User-friendly website
  • Easy signup process
  • Transparent pricing


  • Payroll services cost extra 
  • Live chat feature on website is confusing
  • Customer complaints about cancelation process

Our Verdict

Overall, we were pleased with our Zenefits experience. The site is easy to use, information is readily available, and sign up is fast. The ability to demo the product before committing to a purchase is a huge plus for business owners. 

Our experience with customer service was mostly positive, as we had good interactions with them over the phone and email. However, the live chat feature is a bit confusing. 

Zenefits’ services are an outstanding value and include a variety of features and benefits. The one major downside is that payroll services are an add-on. Bu the pricing is still very attractive and considerably more affordable than competitors. 

3. Paycor

Paycor offers full service payroll, including your tax filings, as well as a variety of additional tools and benefits. Paycor is one of the more expensive providers, yet it also provides robust HR support and services, distinguishing itself from its competitors. 

Pricing and features

The Basic Plan includes full-service payroll, including W-2s and 1099s, and federal, state, and local tax filings. It also offers employee social security number verification and new hire reporting to the state.

Compared to the competition, this plan does not offer as much value. Other industry leaders offer similarly- or lower-priced plans that include health insurance administration, which requires additional payment in the case of this plan. 

This plan offers little value considering the price.

The Essential Plan offers everything in the Basic Plan, with the addition of employee onboarding and HR support. It also offers a month-end accounting package, job costing, 401K processing and integration, and a few other services.

This plan offers much more than the Basic Plan, so it’s a better value. But it’s still more expensive than competing plans that offer healthcare administration for less. 

The Core Plan offers everything in the Essential Plan plus Paycor expense management, Paycor HR, and Paycor Career Management, which is described by Paycor as follows:

“Paycor Career Management provides companies a way to create better career strategies, facilitate internal movement, and identify talent risks. Managers and employees can clearly define role responsibilities and set expectations together so that employees receive feedback that’s specific to them and their growth plan.”

This is a recently introduced service, and if it’s effective, a nice value-add. 

Overall, with HR functions taken care of for you, this plan seems to be a good value, and offers more than competitors. 

The Complete Plan offers everything in the Core Plan with the addition of Paycor Analytics, compensation planning and talent management.

The talent management feature monitors employee performance to collect data for reviews and automates the process of reviewing employees.

It’s an interesting service, and the entire plan seems to offer a robust suite of services that could provide a lot of HR support in addition to the payroll services.

Pros and Cons


  • Information is easy to find on the site
  • Several plan options are available
  • Higher-tier plans offer robust HR services and support
  • Convenient mobile app


  • No online account setup
  • Expensive compared to competitors
  • Customer service is poor, problematic 

Our Verdict

Paycor offers four plans, which give customers more options to choose from than other payroll services. Information is easy to find on the site, and the site is user-friendly. However, you cannot complete the signup process online, which extends the time involved.  

Paycor offers robust HR services in its higher-tier plans compared to the competition, which helps set the company apart. However, if you just need payroll services, Paycor’s Basic plan is expensive.  

Overall, Paycor’s higher-tier plans offer good value, though they include no health insurance administration. If you’re looking for robust HR support, we highly recommend Paycor. But if you only need good payroll processing, we suggest shopping around. 

4. Thomson Reuters Accounting CS Payroll

Thomson Reuters is a Canadian multinational media company. They provide software solutions, and have created Accounting CS Payroll software specifically for accountants. The software allows you to process payroll for multiple clients. It comes included with their CS accounting software, providing an all-in-one accounting and payroll solution for you to manage your clients’ needs.

Pricing and features

The software allows you to enter time tracking information easily and makes all tax calculations for you at the federal state and local levels. You can pay employees by check, direct deposit, or debit card. 

It has integrated tax forms, allowing you to easily file and pay taxes for your clients.  It also automatically generates payroll reports.

It can even handle payroll calculations for clients that have more complex payroll needs, including weighted overtime calculations and child support payment deductions.  It automates many payroll tasks. 

You can license the software for your use in three ways:

  1. Purchase the software and host it in-house
  2. Purchase the software and have Thomas Reuters host it
  3. Lease the software under a Software as a Service (SaaS) model

Pricing is determined by customized quotes. 

Pros and Cons


  • Extremely sophisticated features to handle complex payroll
  • Integrated with accounting functions
  • Trusted brand name
  • Designed specifically for accountants


  • Poor customer reviews
  • Limited customer service
  • No HR tools or services

Our Verdict

As a software designed specifically for accountants, Thomson Reuters offers a number of rich features that make it easy to manage the payroll and accounting functions for multiple clients at once. 

The Thomson Reuters website is quite informative, with all the features of their software clearly detailed. The negative customer reviews on the BBB website are a bit concerning, but there are not many, so we assume that those were isolated incidents.

Overall, based on our experience and research, we confidently recommend Thomson Reuters Accounting CS Payroll. 

What to Look for When Choosing a Payroll Software

With so many payroll services to choose from, it can be difficult to decide which is best for you and your accounting team. There are three essential elements that can help you make your decision.


Each service comes with a variety of features, and their plans are all designed differently. For example, only some providers offer HR tools and support. 

You and your business clients may need some features but not others, so it’s important to choose the service that offers just what you want. If it’s important to you to have HR services, you’ll want a service that offers that feature. But if your accounting staff doesn’t need health insurance administration, on the other hand, you don’t want to end up paying extra for it. 

As an accountant, you’ll certainly want software that can integrate your in—house software. Choose a service that has everything you need to make handling payroll for your clients as easy as possible. 


Of course, you’ll want to get the best value, so it’s a good idea to compare the cost of each service. Plans with more features tend to be more costly, so you’ll probably want to stick with the tier that meets your needs. You’ll also want great customer service, so if you’re considering the cheapest service, check the reviews to see how its customers feel about it. 

Customer Service and Reviews

A good way to learn about the quality of anything you’re buying is to check out what users say about it. When we review services we look at Better Business Bureau** ratings and reviews, as well as TrustPilot reviews. It’s wise to look at both positive and negative reviews to find out what people love about the service, and about issues customers have encountered. 

Remember that fake reviews are common, so you might take some of the reviews with a grain of salt.