Finding the Best Payroll Software for Your Accounting Business

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Manually calculating, filing, and paying payroll is tedious and time-consuming for most businesses. If you’re an accountant, it’s highly unlikely you would be able to manually process payroll for all of your clients while juggling your other responsibilities. Payroll software makes processing payroll much easier compared to doing it manually. You can save time while ensuring accuracy for each employee’s payroll. This makes payroll software for accountants indispensable. 

However, dozens of software options exist, ranging in price and features. We’ll look at how to find the best payroll software for your accounting business and some of the top options you’ll want to consider.

Related: How R&D Credits Help With Payroll Taxes [2023]

How to Choose Payroll Software

When choosing payroll software, you’ll want to consider which will best fit you and your clients’ needs. The one you choose should be quite robust as not only are you handling payroll for your own employees but for each of your clients as well.


The features a payroll program offers can make a significant difference in its usability. A few features are almost required if you’re an accountant, while others are optional yet worth considering.

The availability of direct deposit is a must for any accounting business. Without it, you would need to spend time manually writing and delivering paychecks. This is simply not an option for most businesses.

In a similar vein, tax modules, including payroll tax filing ability, can be key. You don’t necessarily need a program that files payroll taxes for you. But it’s important to look for software that at least calculates and tracks this. Choosing one that files for you is a great option if you can.

Compliance features can help make your job much easier and catch gaps that may be overlooked. Part of this is taken care of when the software automatically calculates and withholds taxes, as it reduces human error. However, it could also include providing forms and documents and double-checking regulations based on location.

Some other features you may want to consider include new hire reporting, ledger reports, and time tracking. While these may not be necessary for all accounting businesses, they may be worth it to you.

Ease of Use

A clunky program can be difficult to work with, taking additional time to get anything done. Luckily, modern software is generally very user-friendly. When choosing a program, make sure it is easy to set up and work with on a regular basis. This can save you time and headaches in the learning process. 

Integrations with other software can also make it easier to streamline your processes. For example, some may sync with your clients’ HR software. Many integrate with general accounting software to automatically add payroll data to your books.

You may also want to consider software that integrates other employee management tasks into the same program. For example, certain programs allow time and attendance to be tracked right within the program.

Depending on the clients you work with, you may even want to choose an option that allows for employee self-service. While this used to be reserved for only large companies, modern payroll software is available that can let you offer this.

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Payroll software for accountants is not cheap. After all, you’re essentially paying for licenses for all of your clients. There are also a variety of pricing models, many of which offer different levels with different features.

When comparing prices, start with the base price. But know that you may need to consider a higher service level to get the features and abilities you want. It’s best to directly compare these prices, as they’ll give you a more accurate representation of the price you’ll pay.

Make sure to be on the lookout for free trials. Many providers offer these, and they can be quite valuable. Using a free trial will allow you to make sure the program actually works for you. Use this time to critically examine it and its features before committing.

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Top Choices for Payroll Software for Accountants

While there are numerous options when it comes to payroll software for accountants, there are a few choices that stand out from the crowd. Each of these includes the basic features we’ve already mentioned. However, they also offer something else that stands out.


Gusto is a great option if you want to offer next-day direct deposit. Under their Plus plan, you can do this. In addition, Gusto offers payments for international contractors, PTO, holiday pay, and lifetime digital paystub access, among other features.


If you’re one of the many accountants already using QuickBooks, adding their payroll option may be the way to go. They offer next-day direct deposit, 1099 contractor management, 401(k) plan management, and tax record management to make taking deductions easier.

Related: 10 Example Goals For Accountants To Start Today

Paychex Flex

Paychex Flex works well for accountants working with larger firms with larger payroll needs. This enterprise solution also offers Paychex Pre-Check, a feature that allows employees to see their scheduled payments. Because they can let HR know about discrepancies, you can reduce errors and boost employee relations.


If your clients often work with contractors, ADP’s RUN may be a great solution. It can handle both W-2s and 1099s, making reporting easier. It also offers direct deposit, a mobile app, and multijurisdiction payroll. Plus, it syncs well with popular accounting programs.


Will you be moving from your current payroll provider to a new one? If so, consider OnPay. They offer free data migration to their new customers. This can save a lot of time and money if you are switching. 

They have reasonable pricing, employee self-service, unlimited payroll runs, and even an HR resources library.

Ready to help your clients get the most back from their R&D expenditures? Learn more about our tax software and how it can make it easier to give your clients a better tax experience!


As remote work becomes more of an option for businesses and employees, accountants must also learn to adapt to the challenges this brings. Remote Global Payroll is on the more expensive end of payroll software but offers global payroll, which can be difficult to find. This includes international compliance and taxation, multicurrency support, and infrastructure for each country it services. If your clients have staff in multiple nations, this may be a good option.

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Find the Best Payroll Software for Your Accounting Business

When looking for a payroll provider, you’ll initially be inundated with options. But, once you carefully consider the features you need, ease of use of each program, and pricing options, you’ll be able to compare them better. Our top choices for payroll software for accountants are a great place to start to find one you’ll love.

Related: 10 Accounting Trends To Know for 2023

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