July 6, 2024
13 min

The Best Payroll Software for Accountants: 8 Top Picks for 2024

Enrich your accounting services with payroll software for accountants. Offer your clients payroll management to save time and boost your firm's profitability.
The Best Payroll Software for Accountants: 8 Top Picks for 2024
Table of contents

Accounting and payroll software go hand in hand. If you're an accountant with employees and you offer payroll services to clients, there's no two ways about it; you need a payroll software. Without it, you'll have trouble keeping track of employee data, and also keeping compliant with payroll rules and regulations.

So you know you need it. But how do you choose which one to buy? There are so many payroll software options out there, many with similar features. No doubt, choosing a cloud-based option is the most convenient option for the majority of accounting firms. But besides that detail, you might find yourself at a loss as to how to choose between software.

Key Takeaways from this Post

Many businesses outsource their payroll management. Subscribing to payroll software for accountants will enable you to offer clients these much-needed payroll management services. This could help you boost your firm's profitability and reliability.
Payroll software comes with tools and features that can ensure you provide a thorough service, while taking up as little of your time as possible. It ensures accuracy, and most have automation features that will greatly enhance your experience with the software.
Keep an eye out for self-service portals within payroll software which allow employees to input the number of hours worked. Plus, add and edit personal information, and request time off.
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This is why we've come up with a list of 8 of the best payroll software solutions for accountants to get stuck into. We researched payroll software and condensed our findings into this (relatively) short article so you can decide which option is right for you.

Introduction to Payroll Software for Accountants

Two hands shaking.

Payroll software is a software used by businesses to pay their staff. It often comes with a range of useful features that makes the payroll system easier, more efficient, and more accurate. With payroll software, you can keep employee data organised and have all the details you need stored within the software so it's easily accessible.

When we talk about payroll software for accountants, it can serve two purposes; to be used by you (or your HR department) to pay your own staff. Or, to be used by you to offer payroll services to clients. Such payroll software is often able to handle large numbers of employees so you can offer a thorough and dependable service.

Why do You Need Payroll Software?

Here are the specific reasons why it's beneficial for accountants to use payroll software within their firms:

Payroll Bureaus

Payroll bureaus are companies that take care of payroll for clients. Many accounting firms double as payroll bureaus to offer a more comprehensive service, generate more revenue, and skyrocket their profit margin. If you're not already offering payroll services to your clients, a good payroll software will enable you to do so with relative ease.

One of the good things about incorporating technology into your business, especially those with aspects of automation, is that they can allow you to offer more to your clients with not much extra effort on your part. That's where payroll software comes in handy.

Save Your Firm Time

A brass alarm clock showing the time 7:20.

Just like software can automate accounting, payroll software can automate aspects of your payroll. However, even if the automation tools are minimal, payroll software will still save you time with its range of features, like time-tracking and data management. You can source the data you need quickly and easily.

And of course, saving time very often equates to saving money because you'll be spending your time on other business-boosting tasks.

Enhanced Accuracy

Payroll software can ensure you pay your and your clients' employees accurately, taking into account tax deductions, pension contributions, and benefits. With there range of tools and features, you'll be confident that you're paying for the precise number of hours worked too.  

Track Payroll Data

Payroll software is convenient for storing, managing, retrieving, and tracking employee data. You can easily access historical pay details and there's a clear paper trail of transactions. This is useful for if you need to perform an audit or settle a pay dispute. Additionally, with a lot of payroll software, employees can access their own data and see their previous payslips, hours worked, and tax deductions.

Key Features of Accounting Payroll Software

An old brass key.

Although features of accounting payroll software vary, there are some key features to look out for that indicate it's worth a consideration:

Pay Calculator

Most payroll software should come with a pay calculator as standard. It wouldn't fare well paying for a payroll software and then having to manually calculate payroll yourself. Therefore, when it comes to managing payroll with a payroll software for accountants, this is one of the main features.

Tax and Benefit Compliance and Deductions

Two other things you really don't want to be calculating and tracking yourself are taxes and benefits. Payroll software should take over this task for you. It'll calculate tax and benefit deductions, ensuring the figures are accurate every time so your (and your clients') business remains compliant.

Pay Distribution

A man putting a credit card into a pay machine.

Payroll software can help with pay distribution. Sometimes this is automatic. And sometimes it gathers all the information so that you can pay manually with just a few clicks. Regardless of which one, payroll software makes the process of actually paying your and your clients' staff much simpler.


Some software has an employee portal which they can access and input their hours worked. Other software has different methods of time-tracking. Either way, time-tracking features of payroll software are really useful because not only do you have a record of hours worked. But, the software also uses that information to calculate pay.

Analytics and Reporting

Payroll analytics help you keep on top of payroll and its associated expenses. You can see where you might be able to cut costs and identify areas which are overly-expensive for you or your clients. You might also be able to use the reporting tools to see where you might adjust your allocation of resources.

Top Payroll Software Options for Accountants

  1. QuickBooks Online Payroll
  2. Xero Payroll
  3. OnPay
  4. Gusto
  5. Patriot Payroll
  6. SurePayroll
  7. RUN Powered by ADP
  8. Paychex Flex

1. QuickBooks Online Payroll

Information about QuickBooks Payroll tax software on the left and on the right is a woman folding her arms and a graph of employee data.

One of the good things about using QuickBooks Online Payroll is that it integrates seamlessly with your accounting software. There are three QuickBooks Payroll options; Payroll Bureau, Advanced Payroll, and Core Payroll. It is a cloud-based solution, making it easily accessible for you, your clients, and their employees.

Key Features

  • Connect QuickBooks Payroll to all the best accounting software, including QuickBooks, Xero, Sage, and Freshbooks.
  • Employees can access their data and update it whenever they need to.
  • Automate aspects of the payroll including pay runs, RTI tracking, pensions, and tax code updates.
  • Access tax features like VAT return submission, VAT errors checker, and income tax estimates.

2. Xero Payroll

Information about how Xero helps you meet HMRC requirements and automates payroll calculations. There's also snapshots of the software.

Being another popular accounting software, Xero also offers a comprehensive payroll solution. It's a HMRC-recognised software and helps UK business's remain MTD-compliant. The software saves you plenty of time each month on admin and other menial tasks. Integrate Xero Payroll with Xero's entire suite of tools, like invoicing, Workpapers, and Practice Manager.

Key Features

  • Employee self service portal allows employees to submit their timesheets, update their details, request time off, and view their payslips.
  • Automatically calculates payroll, including tax, paid leave, and pensions.
  • After each pay run, Xero automatically sends your payroll details to HMRC so you don't need to do it manually.
  • Xero Payroll connects with various pension providers, and facilitates automatic pension enrolment and reenrolment.

3. OnPay

Information about OnPay and a snapshot of the platform in use.

Ideal for U.S accountants, OnPay has a suite of tools to help manage payroll, HR, and benefits. Taxes in the U.S can be more complex than the UK, so having a dedicated payroll solution to help you can really make a positive difference to your service. OnPay is suitable for accountants serving a wide range of industries and types of workers, including remote employees and contractors.

Key Features

  • Variety of payroll calculators, including hourly + salaried, tipped wages, gross-up, flat bonus, and aggregate bonus.
  • Integrates with a range of software including state tax registration, time-tracking, and accounting software like Xero and QuickBooks Online.
  • Customisable employee onboarding tools to ensure you have all the right details about them.
  • Direct deposit payroll allows you to pay employees' wages into their bank accounts with just a few clicks.

4. Gusto

Information about how Gusto facilitates fast, accurate, and effortless payroll on the left and on the right is a man up to a laptop.

Gusto has a partner program for accountants that allows you to access their Payroll solutions for free. You can earn up to $400 for referring clients to Gusto and also enjoy a 20% revenue share. Plus, you can earn special perks for your clients. Another plus point of Gusto is that it does not limit the number of payrolls you complete each month.

Key Features

  • Project management features that allow employees to track time spent on projects, and submit timesheets and hours worked.
  • Helps you keep compliant with state and union laws (even for remote teams) by tracking breaks and overtime.
  • Gusto has customisable reporting tools. Send employees surveys to complete and get reports on employee happiness.
  • Integrate with a large variety of apps, including QuickBooks Online, Asana, Expensify, and DropBox.

5. Patriot Payroll

Information about Patriot Payroll and a man in a shirt folding his arms.

Patriot is a payroll management and accounting software that's known for its user-friendly interface and simplicity. Aimed at U.S customers, the software is reasonably-priced and has an entirely U.S-based support team on-hand to help you. Use accounting and payroll together, and choose Time & Attendance and HR softwares as optional add-ons.

Key Features

  • Flexible billing as accountants choose their subscription, and then pay per client and per employee.
  • An onboarding platform that shows you your clients' data and which clients you still need information from.
  • Plenty of payroll reports available to view and filter through, including tax deposits, paycheck history, time off, and assigned deductions.
  • Both files and deposits local taxes for your clients and employees.  

6. SurePayroll

On the left is a form to sign up to SurePayroll and on the right is a woman writing something in front of a laptop. The background is green.

SurePayroll is another one for U.S-based accountants. It's an intuitive payroll manager with impressive, productivity-boosting features. It even offers a guarantee (subject to terms and conditions) that users wont face tax filing penalties. The Full Service payroll plan offers a complete tax filing service which includes the filing and depositing of federal, state, and local taxes.

Key Features

  • Save loads of time with automatic payroll. You get reminders before payments are made and you get the flexibility of switching payments off whenever needed.
  • A white label solution so you can easily incorporate your own branding elements into the software.
  • Integrates with your accounting software like QuickBooks Online, Zoho Books, or Sage Accounting.
  • Get SurePayroll for free if you have ten clients or more.

7. RUN Powered by ADP

Information about RUN Payroll on the left and a man on the left wearing a suit and smiling. He has an open laptop.

RUN is a payroll processing software that caters to small businesses and medium-enterprise businesses worldwide. The company gives a useful, one minute overview video of the product as well as a very handy interactive demo, which you can access after entering your email address into the system. RUN offers round-the-clock support via phone call and live chat. Plus, their experts will also help you get up and running.

Key Features

  • RUN software keeps up to date with tax regulations so its tax deductions from wages are always accurate.
  • ADP mobile app makes payroll management convenient and also makes it easy for employees to submit their details and hours.
  • Integrates with different business software, time-tracking solutions, and HR systems.
  • Lots of calculators and tools to use, including hourly paycheck calculator, 401(k) contribution calculator, ACA penalty estimator, and employer paycard savings calculator.

8. Paychex Flex

Information about three Paychex Flex plans and a computer displaying each solution.

As you might gather from the name of this software, Paychex Flex offers a flexible payroll service. The software is ideal for businesses of all sizes, as well as accountants looking to boost their revenue by taking on payroll clients. Paychex employs compliance experts who will help you and your clients keep on top of federal, state, and local tax obligations.

Key Features

  • Taxpay is an automated tax administrative solution that calculates pay and taxes, and files taxes according to where they need to go.
  • Paychex Flex offers 24/7 expert support through telephone and live chat.
  • Comes with a huge array of optional add-ons so you can tailor your plan to suit you and your payroll clients.
  • Provides employees with financial wellness assistance which allows them to access resources that'll help them reach their financial goals.

Selecting the Best Payroll Software for Your Needs

A fabric man holding a green tick and a beige fabric background.

Here are some criteria to consider to help you select the best payroll software for accountants:

Integration With Accounting Software and Other Solutions

Integrating your payroll service with your accounting software will help you keep organised, your data synced, and your details accurate across the board. Additionally, being able to integrate payroll with your other software for accountants, like expense management for example, will allow you to create a streamlined system of processes across your whole operation.


A woman with her arms in the air in front of a computer that says 'payroll' on the screen.

There are lots of features that make payroll systems worth the investment for accounting firms. Obviously, you want to process payroll, and get accurate tax and payroll calculations for all your payroll clients. However, there are also other tools and features to think about.

For example, self service portals, being able to complete unlimited payroll runs, and direct access to pension schemes. Brainstorm a list of essential features, not-needed ones, and nice-to-haves.

Self-Service Portal

Giving client employees access to their own self service portal will save you a lot of time with chasing up timesheets. It will also minimise the number of documents and filing you need to manage as it will sync up with the data in your payroll dashboard. A self-service portal will help keep your clients satisfied and show them you're a forward-thinking accounting firm.


The usability of the payroll solution is a pretty big consideration, for both you and your clients. The last thing you want is to make things complicated for clients, especially when they don't need to be. Some software are more complex than others. For example, QuickBooks Payroll Bureaux is not quite as straightforward as Xero. Try out demos where you can, read user reviews, and weigh up your options for features vs usability.


Someone on a calculator and pointing to a document.

This pretty much goes without saying. Your budget will likely play a part in choosing what payroll software to use. Also consider the cost of any add ons and features that come at a higher cost.


When we talk about limitations, we're referring to a limit to the number of clients, payment schedules, and features that a software imposes. Also look at how easy it would be to upgrade your subscription as your client base grows. If a software is only suitable for small businesses, for example, you might need to migrate down the line.

How Can Link My Books Boost Your Accounting Firm?

Information about finding an eCommerce accountant with Link My Books and on the right are a woman's hands and a laptop.

Link My Books boosts your accounting firm by enabling you to automate your clients' bookkeeping. It sits in between your accounting software and your clients' sales channels, and transfers financial data to your accounting software automatically.

Key Link My Books Features

  • Profit and loss statements: Link My Books categorises your clients' data, breaking it down into profits and losses. Get a clear view of sales, refunds, shipping fees, and advertising fees, amongst other data. This information is all transferred to your accounting software automatically.
  • Benchmarking: Link My Books Benchmarking undertakes a cohort analysis of sales data to give users a percentile ranking for their business's performance. It measures metrics like sales growth, refunds ratio, and fee ratio against industry averages.
  • Accurate tax calculations: When you set up your Link My Books account and connect your clients' sales channels, you'll be asked a few questions that'll help the software determine the correct tax rates. Once set up, the correct tax rate will be applied to every product your clients sell.
  • P & L by Channel: This is another reporting feature. But this time, you can compare the performance of your clients' different sales channels. View data like sales and refunds across different channels with side-by-side comparisons. Understand which channels are performing best and where clients might be wasting money.

Final Thoughts on Choosing the Best Payroll Software for Your Needs

A white cloud on top of a blackboard.

Many payroll systems are relatively similar to one another. For those that are, this is where details like user-friendliness and integrations can help differentiate between them so you're better able choose the best one for your needs. Payroll tax and calculations are normally must-haves.

But there are also more advanced features within payroll software for accountants that might sway your decisions, such as pension management, mileage tracking, or being able to run multiple payment schedules at the same time.

If you're into time-saving software for accountants, Link My Books is a user-friendly and intuitive software that lets you put your clients' bookkeeping on autopilot. You can set it to automatically transfer data from eCommerce platforms to your accounting software. This will save you a massive six hours per month on every one of your eCommerce clients.

Sign up for your free trial today and add automated bookkeeping to your services. Transform your bookkeeping processes with Link My Books.

Link My Books 4 day free trial.
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