As an accountant, you need payroll software that syncs with your clients’ existing accounting software, automates as many aspects of payroll as possible, and simplifies tax season. You also need user-friendly payroll software that easily accommodates data from multiple clients while reducing the possibility of user error.
SEE: The four best free payroll software options available in 2023.
Each option on our list of the best payroll software for accountants meets those requirements and then some. Keep reading to find the right software for your unique accounting and payroll needs.
- Top payroll software for accountants feature comparison
- Top payroll software for accountants
- Key features of payroll software for accountants
- How do I choose the best payroll software for my accounting business?
Top payroll software for accountants feature comparison
Whether you’re part of an in-house accounting team or you manage multiple client accounts at your accounting firm, your payroll software should accurately file taxes and calculate paychecks so you can keep your clients’ business finances in line. Ideally, CPA payroll software also helps you communicate complicated financial concepts to non-accountant business owners.
Learn more about the features to look for in payroll software for accountants in our comparison chart below.
|Full-service tax filing
|Professional account migration
|Accounting software integrations
|Accountant partner pricing discounts
|Free marketing material
|Starting monthly price
|Yes (Elite plan only)
|$45 plus $5 per employee
|$40 plus $6 per employee
|Yes (Premium plan only)
|QuickBooks, Xero, FreshBooks, Sage, and more
|$40 plus $6 per employee
|QuickBooks, Xero, Sage, and Oracle NetSuite
|$39 plus $5 per employee
|QuickBooks, Xero, Sage, and Oracle NetSuite
|Custom quote only
|Yes (full-service plan only)
|Patriot Accounting, QuickBooks Online
|$35.15 + $3.80 per employee
|RUN Powered by ADP
|QuickBooks, Sage, Xero, Wave
|Custom quote only
QuickBooks Payroll: Best overall
QuickBooks Payroll, Intuit QuickBooks’ payroll product, includes the full spectrum of features accountants need to process payroll for their clients. Most notably, each plan includes full-service payroll, next-day direct deposit and optional add-on healthcare benefits (available in every U.S. state except Hawaii and Virginia). Like Gusto Payroll, Paychex and other payroll software services, QuickBooks Payroll mails out 1099 and W-2 forms at the end of the year and includes an autopilot feature that lets you schedule payroll in advance.
QuickBooks Payroll’s biggest benefit is its seamless integration with Intuit QuickBooks Online, one of the most widely used accounting software tools in the world. Since QuickBooks Online was made with non-accountant, small business owners in mind, many of your clients likely use it already, which can make them feel more comfortable adding payroll software to their roster.
Accountants who partner with QuickBooks Online Payroll are known as QuickBooks ProAdvisors. Through the QuickBooks ProAdvisor Preferred Pricing program, you can choose to have QuickBooks bill your accounting firm directly at a discounted rate, or you can pass savings along to your client with a year-long ProAdvisor discount.
Without the QuickBooks ProAdvisor discount, QuickBooks Online Payroll pricing is as follows:
- Core costs $45 a month plus $5 per employee per month.
- Premium costs $75 a month plus $8 per employee per month.
- Elite costs $125 a month plus $10 per employee per month.
New customers can choose a 30-day free trial or waive the free trial to get 50% off for three months. (The discount applies to the base price only, not the per-employee fee.)
- Automatic next-day direct deposit with QuickBooks Payroll Core or same-day direct deposit with all other plans.
- Optional employee benefit add-ons including healthcare and 401(k) plans.
- Automatic wage garnishment deduction.
- PTO management.
- Preferred partner discounts for both QuickBooks Payroll and QuickBooks Online.
- Problem-free syncing with QuickBooks Online.
- No additional fee for state and federal payroll tax filing. (Additional fee for local tax filing.)
- Comprehensive payroll features on a streamlined, user-friendly platform.
- No workers’ compensation administration with QuickBooks Payroll Core.
- White-glove setup only available with QuickBooks Payroll Elite, the most expensive plan.
- Limited human resources features, tools and support.
For more information, read our full QuickBooks Payroll review.
OnPay: Best free data migration
OnPay’s thorough blend of payroll and HR features makes it the ideal payroll software solution for businesses that want one all-inclusive service to manage employee pay and benefits. Along with unlimited monthly payroll runs, OnPay offers employee self-service onboarding tools, automatic state new-hire reporting and access to a generous HR library that helps business owners stay legally compliant.
If you or your client switches to OnPay from another payroll provider, OnPay’s in-house team of experts will set up the software for you to ensure accuracy during the transition. OnPay has the added benefit of syncing with QuickBooks Online, QuickBooks Desktop and Xero, another of the most popular accounting software programs for enterprises.
If you partner with OnPay to manage your clients’ payroll, you can use OnPay’s payroll service for free for your own firm. Additionally, once you have at least three clients, you’ll qualify for software discounts you can pass along to those clients.
Outside of partner pricing discounts, OnPay charges a flat fee of $40 a month plus $6 per employee per month. Every new client can use OnPay free for one month.
- Specialized payroll plans for businesses in niche industries, including payroll for nonprofits, restaurants, farms, churches and enterprises.
- Workers’ compensation administration in all 50 U.S. states.
- Healthcare and dental insurance benefits in all 50 U.S. states.
- Direct deposit, paper check and prepaid debit card employee pay options.
- Free marketing tools for your accounting firm.
- Free migration and white-glove account setup.
- Upfront flat-fee pricing with no hidden fees.
- Free multi-state payroll runs.
- Integration with most popular time tracking software tools.
- One plan only, which limits scalability for growing businesses.
- No international payroll or HR features, including for employees based in U.S. territories.
For more information, read our full OnPay review.
Gusto: Best for versatile accounting software integrations
Gusto is one of the most-used payroll services in the United States. Unlike QuickBooks Payroll, Gusto Payroll integrates with multiple accounting software tools for small businesses and enterprises alike. Whether you or your clients use Aplos, Bookkeeper360, AccountingSuite, Ignition, Paperclip, Sage Accounting, Xero, FreshBooks or a host of other accounting, ERP and HCM solutions, you can sync that software seamlessly with Gusto.
As long as you onboard at least one new client to Gusto per year, your accounting firm can use Gusto’s Plus plan for free in-house. If you have three or more clients, you qualify for product discounts that range from 10% to 20%.
While each of Gusto’s three plans have the same payroll features, the higher-priced plans include far more HR resources:
- Simple costs $40 a month plus $6 per employee per month.
- Plus costs $80 a month plus $12 per employee per month.
- Premium has exclusive pricing only.
Gusto doesn’t advertise a free trial on its site, though many third-party sites report that Gusto does offer one.
- Free marketing collateral for Gusto-partnered accounting firms.
- Next-day direct deposit with Gusto Simple and same-day direct deposit with all other Gusto plans.
- Optional employee health insurance benefits and administration in 37 U.S. states.
- Hiring and onboarding tools, including offer letter templates and employee self-onboarding features.
- International independent contractor payments (for an additional fee).
- Built-in time tracking (not available with the cheapest plan).
- Automatic pre-scheduled payroll runs.
- Custom admin workflows and permissions with each plan.
- Compliance alerts, HR resource library and HR expert access limited to the most expensive plan only.
- Health insurance limited to 37 U.S. states.
For more information, read our full Gusto review.
Paychex Flex: Best accountant-specific resource library
Paychex Flex has more perks for accounting firms than almost any other payroll software program. Paychex’s accountant partners can access Paychex’s comprehensive accountant knowledge center (which includes resources like the U.S. Master Tax Guide), free accountant publications and an extensive end-of-year resource center. Paychex also offers online courses and webinars for accountants who want to earn free continuing professional education credits.
Other Paychex resources for accountants include direct access to a dedicated Paychex HR team, who can help you answer your clients’ questions about hiring and labor laws. If you want to position your firm as an expert in general business consulting, Paychex can give you the tools to do so.
Paychex doesn’t advertise any discounts that Paychex-affiliated accountants can pass along to their clients. Additionally, while Flex has three separate payroll plans, it only lists pricing for its cheapest plan online:
- Paychex Flex Essentials costs $39 a month plus $5 per employee per month.
- Paychex Flex Select and Paychex Flex Pro require custom pricing quotes.
Paychex’s free trial of three months is longer than most other free trials in the industry.
- Thorough HR and payroll educational resources for accountants to pass along to their clients.
- Automatic payroll tax calculation and filing with on-demand assistance from a dedicated Paychex representative.
- Employee- and employer-facing apps with self-service portal and self-guided onboarding.
- HR library access for both accountants and their clients.
- Automatic state new-hire reporting.
- Thorough suite of accountant-specific benefits, including access to a comprehensive knowledge center.
- Extensive compliance updates and support.
- Three-month free trial for most new clients.
- 24/7 customer support.
- Limited pricing transparency.
- Additional fee for accounting software integration and wage garnishments.
For more information, read our full Paychex review.
Rippling: Best for global payroll management
Rippling is a fully featured global HR, IT and payroll solution. Unlike both OnPay and QuickBooks Payroll, Rippling supports international payroll, including payments to both contractors and in-house employees (in contrast, Gusto only supports international contractor payments.) Rippling is also the only payroll and HR software on our list to provide remote tech management. Its IT module lets businesses configure business software from afar, which makes it a good choice for accounting firms whose clients are enterprises with remote, global workforces.
In order to build a customized Rippling package, you have to first start with Rippling’s software platform, Rippling Unity, which costs a monthly base fee of around $35. From there, you can add whichever Rippling modules you want, from payroll to remote tech management. Each module costs an additional per-employee fee, so Rippling’s costs might add up too quickly for small businesses with tight budgets.
- Thorough payroll automation and integration with native time and attendance software.
- Employee benefits administration.
- Remote app and employee device management.
- Corporate cards and employee expense management.
- Dedicated Rippling support team for accountants only.
- Comprehensive HR, IT and payroll management from one streamlined platform.
- Multiple safeguards to minimize the potential for human error during data entry.
- No transparent pricing on site.
- Limited information about accountant-specific perks available online.
For more information, read our full Rippling review.
Patriot Payroll: Best for small-business payroll
If your accounting firm primarily manages payroll for small and midsize businesses, Patriot Payroll can keep payroll costs low for both you and your clients. While many other payroll providers only offer software discounts once you have five or more clients, Patriot offers a 5% discount for accounting firms right off the bat. Similarly, every accounting firm that works with Patriot gets free co-branding, a benefit that most other payroll systems reserve for firms with at least five clients.
Patriot has both a full-service plan and self-service plan, though its site only lists discounted accountant pricing for the full-service plan:
- Accounting firms with one to five clients pay $35.15 per month plus $3.80 per employee.
- Firms with six to 20 clients pay $33.30 per month plus $3.60 per employee.
- Firms with 21 to 50 clients pay $31.45 plus $3.40 per employee.
- Firms with 51 to 100 clients pay $29.60 per month plus $3.20 per employee.
Accounting firm clients also save on Patriot’s accounting software. Larger accounting firms with 100+ clients are eligible for deeper discounts.
- Fully customizable payroll reports specific to each client.
- 30-day free trial for all new client accounts.
- Automatic multi-state tax filing (additional fee).
- Free setup and onboarding for every new client.
- Payroll and accounting software discounts for accounting firms working with one client only.
- Extremely user-friendly dashboard for easily managing hundreds of clients.
- Unlimited users, user workflows and admin permissions.
- Highly rated U.S.-based customer support.
- Extremely limited human resource tools.
- No healthcare benefits administration options.
- Accounting software integration limited to QuickBooks Online or Patriot’s proprietary software.
- No mobile payroll app.
For more information, read our full Patriot Payroll review.
RUN Powered by ADP: Best for growing accounting firms
Most payroll software companies offer marketing perks to partnered accounting firms, but ADP’s marketing tools are a cut above. Its free resources include marketing brochures, customizable videos and firm profiles on sites like TaxBuzz and CountingWorks. Accounting partners can also use the CountingWorks Pro Marketing Suite to establish a company newsletter, create a comprehensive website and learn how to communicate better with clients.
Like Paychex, ADP helps accountants register for continuing professional education courses. It also ensures access to IRS credit courses that likewise boost your business’s credibility and expertise.
ADP doesn’t list any pricing information online. To learn how much RUN Powered by ADP costs and whether the company offers accounting partner discounts, contact ADP directly to request a quote.
- Automatic paycheck calculation, tax filing and state new-hire reporting.
- HR tips, checkups and newsletters with every plan.
- Built-in time and attendance software with automatic payroll syncing.
- HR features included with every payroll plan.
- Well-reviewed mobile app for employees and employers.
- Add-on benefits like retirement accounts, healthcare and workers’ compensation administration.
- No transparent pricing online.
- Compliance alerts and HR database only available with pricier plans.
- Additional charge for W-2 and 1099 delivery.
For more information, read our full ADP review.
Key features of payroll software for accountants
At bare minimum, all accounting payroll software should include free unlimited payroll runs, paycheck calculation, tax filing, direct deposit and employee pay stub access. But the best payroll software for accountants should go above and beyond the basics to offer perks specific to accounting firms. Whether you manage one client or hundreds, look for a payroll solution that prioritizes the following features and services:
Professional account migration or white-glove setup
Your clients will likely need your help moving their payroll data from their old payroll system to your system (or with setting up payroll for the first time if they’ve just hired an employee.) While you can take care of data migration by hand, it’s a time-consuming process that requires a good deal of oversight to reduce errors.
The top accountant payroll providers should offer free data migration services, meaning their team will set up your clients’ payroll software on your behalf. This professional setup should include multiple quality checks to mitigate the possibility of introduced errors.
Accounting software integration
Your payroll software should be completely compatible with your preferred accounting solution. The two should sync automatically and update in real time. Otherwise, you risk sharing inaccurate data with your client. Additionally, if you have to enter financial payroll data into your client’s general ledger by hand, you’ll need to double- and triple-check that you entered the data accurately.
Most payroll software syncs with at least one accounting solution and all of the most popular accounting payroll products integrate seamlessly with QuickBooks Online. If you or your clients use accounting software other than Intuit QuickBooks, make sure it integrates with your payroll service of choice.
Completely automated full-service payroll
When you’re juggling multiple clients with different pay schedules, software with automatic payroll runs, fully automated direct deposit and autopilot or one-touch payroll processing can save you hours of time. To free up time for more important accounting tasks, look for payroll systems that thoroughly automate most, if not all, payroll processes.
Discounts and promotional material for accounting partners
Whenever you onboard a new client, you aren’t just bringing in more business for your firm: You’re also bringing your payroll provider a new customer and source of income. The best payroll software companies will treat you like a true partner, offering discounts (or freebies like letting your firm use the software for free), promotional material and other accountant-specific benefits.
Dedicated customer support
Since you’re dealing with multiple client accounts, a problem with your payroll software doesn’t impact just one business owner: It potentially impacts dozens of businesses and hundreds of employees who are counting on you to ensure they get an accurate, timely paycheck.
Instead of routing you to a phone tree or responding only via email, your payroll software provider should have a dedicated customer support team specific to accounting firms. Be wary of any payroll provider that doesn’t advertise its commitment to answering accounting firms’ questions as soon as possible.
To find the best payroll software for accountants, we looked at the most popular, best reviewed software on the market. We narrowed down the playing field by assessing each payroll provider’s accountant-specific tools, features, and perks. We looked at verified user reviews, viewed demos and spoke with sales representatives when possible.
How do I choose the best payroll software for my accounting business?
The best payroll software for your accounting business will be versatile enough to meet your firm’s in-house payroll needs while accommodating your clients’ needs as well. It will sync seamlessly with your accounting software so your clients’ financial data is always accurate and up to date. It will fall within both your budget and your clients’ budgets and it should scale to keep pace with the size of your clients’ businesses.
Keep these considerations in mind as you search for the right payroll software for your needs. Don’t be afraid to insist on a demo or free trial before you commit to one payroll provider over another. The payroll software you choose will have a huge impact on your business’s ability to turn a profit as well as your clients’ happiness, so weigh your options thoroughly and ask your sales representative as many questions as possible while making your decision.