Best Payroll Software for Accountants in 2023
Charlette has over 10 years of experience in accounting and finance and 2 years of partnering with HR leaders on freelance projects. She uses this extensive experience to answer your questions about payroll.
Robie has more than five years of content writing experience and specializes in writing about payroll and human resources software for small businesses.
This article is part of a larger series on Payroll Services.
The best payroll software for accountants makes it easy to handle payroll for many clients. It should integrate with accounting software, have a dashboard to manage multiple clients, and offer benefits specific to the needs of certified public accountants (CPAs). Below are our seven top-recommended payroll software for accountants.
- QuickBooks Payroll for Accountants: Best overall payroll software for accountants and those needing fast direct deposits
- Gusto for Accountants: Best for small business full-service payroll and advertising accountant payroll solutions
- Rippling for Accountants: Best human resources (HR), payroll, and information technology (IT) tools to manage remote employees
- OnPay for Accountants: Best for client migration support and managing payroll duties
- Patriot Payroll for Accountants: Best accountant payroll software with increasing discount perks
- Paychex for Accountants: Best payroll processing software for accountants wanting continuing education perks
- SurePayroll for Accountants: Best affordable payroll accounting software for simple pay runs
Best Payroll Software for Accountants Compared
Free Trial | Starter Monthly Pricing | Contractor-only Payroll Plan | Additional Fees for Payroll Tax Filings | |
|---|---|---|---|---|
 | 30 days | $5 per employee plus $45 base fee | $15 monthly for 20 workers; plus $2 for each additional worker | Local tax filings available only in higher tiers |
 | ✕ | $6 per employee plus $40 base fee | $6 per employee plus $35 base fee monthly | ✕ |
 | ✕ | $8 per employee plus $35 base fee** | ✕ | ✕ |
 | One month | $6 per employee plus $40 base fee | ✕ | ✓ (if you want OnPay to print and mail W-2/1099 forms) |
 | 60 days | $4 per employee plus $37 base fee*** | ✕ | ✕ |
 | Three months* | $5 per employee plus $39 base fee | ✕ | ✓ (contact Paychex for a quote) |
 | Up to six months* | $5 per employee plus $29.99 base fee*** | ✕ | $9.99 for local tax filings in OH and PA |
*This promotion can end at any time. Visit the providers’ websites to view the latest promos on offer.
**Pricing is based on a quote we received; includes Rippling’s workforce management, payroll, and time tracking solutions.
***These represent fees for Patriot Payroll and SurePayroll’s full-service plan with tax filing services. Both providers also offer a do-it-yourself option, where you handle tax filings yourself.
Free Payroll Software For Your Firm | Special Discounts for Clients and Accountants | In-house Accounting Solution* | Other Perks | |
|---|---|---|---|---|
| ✓ | ✓ | ✓ |
|
| ✓ | Accountants can pass discounts to clients | None |
|
| ✓ | ✓ | None |
|
| ✓ | Accountants can pass discounts to clients | None |
|
| If you have six or more clients | Accountants only | ✓ |
|
| ✕ | Accountants only | None |
|
| If you have 10 clients | Accountants only | None |
|
*Access to the providers’ accounting software may require additional fees.
All the payroll systems we reviewed provide the essential tools that accountants need to process client payroll, such as salary calculations and deductions, direct deposit payments, and tax administration services. These providers also offer access to employee benefits plans (except Patriot Payroll), new hire onboarding, and employee self-service tools. Below are some of the key features.
Multistate Pay Runs | Standard Direct Deposit Timelines | Health Benefits Available in 50 States | Time Tracking Tools | |
|---|---|---|---|---|
| ✓ | Next day | HI, VT, and DC aren’t covered | Included in higher tiers |
| Included in higher tiers | Two and four days | 37 states only | Included in higher tiers |
| ✓ | Two days | ✓ | Included in quote |
| ✓ | Two and four days* | ✓ | Via third-party integration |
| ✓ (additional state tax filings cost $12 per state) | Two days for qualified companies | ✕ | Paid add-on |
| ✓ | Two days | ✓ | Paid add-on |
| ✓ (charges $9.99 for multi-state tax filings) | Two days | ✓ | Via third-party integration (costs extra) |
*Eligibility for either two- or four-day direct deposits is based on OnPay’s risk assessment
Which Payroll Software for Accountants is Right For You?
QuickBooks Payroll: Best Overall Payroll Software for Accountants
Overall Score:
4.63 / 5
Pros
- Unlimited pay runs
- Fast direct deposits with next- and same-day options
- Robust tax penalty protection
- Integrates seamlessly with QuickBooks Accounting
- Discounted payroll plans for clients plus free payroll software access for accounting firms (requires signing up for its free QuickBooks Online Accountant tool)
Cons
- Must use QuickBooks for accounting
- Basic human resources (HR) features only
- Tax penalty protection is available only in the Elite plan
- Local tax payments and filings are not included in the basic Core tier
QuickBooks Payroll Pricing
Core: $45 + $5 per employee monthly
- Includes full-service payroll, next-day direct deposit, federal and state tax filings, and access to 401(k) plans and benefits
Premium: $75 + $8 per employee monthly
- Core + same-day direct deposit; tax filings in all levels, time tracking, workers’ comp administration; and HR support center
Elite: $125 + $10 per employee monthly
- Premium + project tracking, personal HR advisor, expert setup, and tax penalty protection up to $25,000 per year
Contractor payments: $15 monthly for 20 workers; plus $2 for each additional contractor
- Includes next-day direct deposits, unlimited 1099 e-filings, and a self-setup solution for creating online contractor accounts
Visit QuickBooks Payroll for Accountants
If you use QuickBooks for your clients, then we highly recommend QuickBooks Payroll for Accountants. It lets you set client permissions, guarantees tax accuracy, and includes 24/7 support—plus, its accounting and payroll modules sync seamlessly.
If you sign up for its free QuickBooks Online Accountant solution, you can access your clients’ QuickBooks accounts easily to check their books, edit transactions, and address issues. It even comes with free access to QuickBooks Payroll Elite, which you can use to pay your employees, discount pricing for your clients, a revenue share option, and a partner ProAdvisor program with preferential rates for both you and your customers. Visit its website to find out more about its ProAdvisor program.
Since Our Last Update:
QuickBooks has launched a Contractor Payments package that’s optimal for businesses with only contract workers. For $15 per month, you can process payments for up to 20 workers (plus $2 for each additional contractor), e-file 1099 forms, and pay contractors via next-day direct deposits.
Scoring an overall of 4.63 out of 5 in our evaluation, QuickBooks Payroll for Accountants earned high marks (4 and above) in nearly all of our criteria given its solid accounting and payroll solutions, ease of use, robust reporting, and transparent pricing. Users also appreciate its efficient payroll tools as it helps simplify employee pay processing. However, its limited HR tools prevented it from getting a perfect rating because, unlike Gusto and Paychex, QuickBooks doesn’t have a suite of HR solutions for managing the entire employee lifecycle.
QuickBooks Payroll for Accountants provides you with a dashboard where you can track all of your clients’ payroll transactions. (Source: QuickBooks Payroll)
QuickBooks Payroll Overview
If you want to learn whether its payroll functionalities can handle your clients’ pay processing needs, then read our QuickBooks Payroll review.
Gusto: Best for Small Business Payroll & Advertising Payroll Services
Overall Score:
4.41 / 5
Pros
- Integrates with several accounting programs
- Partner program for accountants has a revenue share option and a dedicated account representative
- Access to free marketing collateral to advertise your payroll services
Cons
- Lacks an in-house accounting system
- Health insurance coverage limited to 39 states
- Time tracking and next-day direct deposits available only in higher tiers
- Lacks special discounts for clients (unless accountants opt to pass discount perk to customers)
Gusto Pricing
Simple: $40 + $6 per employee monthly
- Includes full-service payroll, tax filings, single state pay processing, two- and four-day direct deposits, employee benefits, offer letter templates, new hire reporting, onboarding, and basic support
Plus: $80 + $12 per employee monthly
- Simple + next-day direct deposits, time and paid time off (PTO) tracking, applicant tracking, basic job postings, multi-state payroll, and full support with extended support hours
Premium: Custom priced
- Plus plan with additional access to performance reviews, surveys, full-service payroll migration, HR advisers, a dedicated account manager, and a direct line for priority phone and email support
Contractor-only plan: $35 + $6 per contractor monthly
- Full-service payroll, four-day direct deposits, and state new hire reporting
Gusto is a highly rated and popular payroll service that provides solid pay processing and HR support. It offers an accountant partnership program that goes beyond supplying client payroll and includes certification programs and marketing venues for getting more clients. With Gusto Plus, you get a client dashboard and tools to help you serve your customers well.
Since Our Last Update:
The coverage of Gusto’s health benefits has changed—from 39 states to 37 states. Gusto has also increased pricing for its contractor-only payroll plan, from $6 per worker monthly to $35 plus $6 per worker monthly. As part of a new promo, new clients will get discounted pricing of only $6 per contractor monthly (no base fee) for the first six months. After this period, you will be charged the regular monthly fee. Note that this promotion can end at any time—please check Gusto’s website for the latest promo on offer.
In our evaluation, Gusto earned an overall rating of 4.41 out of 5, with perfect scores in pricing, popularity, and reporting capabilities. It lost some points for fewer HR features than others on our list and not providing insurance in all 50 states (unavailable in Alabama, Alaska, Hawaii, Louisiana, Mississippi, Montana, Nebraska, North Dakota, Rhode Island, South Dakota, Vermont, West Virginia, and Wyoming), although it does offer online onboarding. However, users still love its efficient payroll and tax filing services, plus they find its features robust given its price.
Gusto Pro’s dashboard shows a list of “Action Items” to help you run payroll and manage client accounts. (Source: Gusto)
Gusto Overview
For more information about the platform’s payroll, benefits, and HR features, check out our Gusto review.
Rippling: Best Payroll Software for Accountants With Clients Looking for Payroll, HR & IT Tools
Overall Score:
4.35 / 5
Pros
- Payroll, IT, and HR tools are modular—you can select solutions that you need
- Robust integration options with more than 500 apps
- Partner program includes discounts for clients and accountants
Cons
- You need to get its core workforce management platform before you can buy other solutions
- Pricing isn’t all transparent
- Purchasing all of its tools can get pricey
Rippling Pricing*
Software fee: $35 + $8 per employee monthly
- Includes access to Rippling’s core workforce management platform plus full-service payroll and time tracking solutions
App, device, and computer inventory management: $8 per employee monthly
- IT tools to manage business apps and computer provisioning and deprovisioning processes
Benefits administration: Pricing is based on your insurance broker
HR help desk: Custom priced
- One-on-one email/phone support from HR experts
*Pricing is based on a quote we received.
Compared to the other providers in this guide, Rippling allows you to provide clients with a wider range of solutions given its modular HR, payroll, benefits, and IT tools. It even has efficient computer devices and apps provisioning and deprovisioning processes plus Rippling can store your unused computers in its warehouse for safekeeping.
However, its partner accountant program isn’t as robust as Paychex’s with its continuing professional education (CPE) webinars. Aside from a client dashboard, Rippling only provides discounts for your clients and free payroll, dedicated support, and HR tools for your firm.
Since Our Last Update:
In addition to its expense management tool, Rippling has released a corporate credit card that your client’s employees can use for business-related purchases. It even comes with custom policies to help you track and control credit card spending. A global payroll has also been added to Rippling’s suite of solutions, as well as employer of record (EoR) services to help you hire and pay employees in more than 100 countries.
Scoring an overall of 4.35 out of 5 in our evaluation, Rippling received ratings of 4 and up in nearly all of our criteria, with perfect marks in reporting and popularity. Many users like its intuitive interface and the seamless integration between its products. However, its paid HR advisory services and lack of a dedicated payroll specialist (similar to what Paychex offers to its clients) prevented Rippling from ranking higher on our list.
Rippling has a centralized “Client Command Center” for viewing reminders, generating reports, and running client payroll. (Source: Rippling)
Rippling Overview
For a more detailed look at its functionalities, see our Rippling review.
OnPay: Best for Client Migration Support & Managing Payroll Duties
Overall Score:
4.26 / 5
Pros
- User-friendly interface
- Free payroll for your firm with no client minimums
- Partner program for accountants include discounts and revenue sharing options
Cons
- Access to two- or four-day direct deposits depends on OnPay’s risk assessment
- Limited third-party software integrations
- Year-end tax report printing and mailing services cost extra
- Lacks an accounting solution
OnPay Pricing
Software fee: $40 + $6 per employee monthly
- Includes full-service payroll, tax filings, unlimited pay runs, multi-state payroll, offer letters, onboarding, new hire reporting, employee benefits, paid time-off (PTO) management, custom reporting, and self-service tools
OnPay lets you provide clients with payroll, essential HR tools, and benefits options available in all 50 states. Its software has six levels of system permissions (more robust than the other providers in this guide), allowing you to manage client payroll and user access efficiently as well as delegate pay processing tasks, such as payroll approvals, to customers. If you want to streamline HR tasks across multiple business software like accounting, consider Rippling, as it offers customizable workflow triggers that work with its 500-plus partner systems.
For its accountant partner program, you get a client dashboard and an incentive scheme that lets you choose between revenue sharing and discounted pricing. What we like best about OnPay for Accountants is that you get free payroll software for your firm without having to meet client limits or add a customer to your client base every year (like QuickBooks Payroll). It even offers free account setup and data migration services, such as setting up your dashboard, adding client info and employee data, and inputting prior wages into its system.
The platform earned an overall rating of 4.26 out of 5 in our evaluation. It received scores of 4 and above in nearly all of our criteria, given its HR functionalities, reporting capabilities, efficient payroll tools, and affordably priced plan that many users appreciate. It would have ranked higher on our list had it offered an in-house accounting software like QuickBooks and Patriot do.
A screenshot of OnPay’s dashboard for payroll accountants (Source: OnPay)
OnPay Overview
Head to our OnPay review to find more to like about this platform.
Patriot Payroll: Best for Accounting Firms That Want Increasing Discount Perks
Overall Score:
4.18 / 5
Pros
- Affordably priced plans
- Discounts of up to 20%
- In-house accounting solution
- Free access to its payroll and accounting systems if you have six of more clients
- Cobranding throughout its software
Cons
- Limited HR tools
- Interface is not customizable
- Multistate filings cost extra
- Lacks employee benefits option
Patriot Payroll Pricing
Full Service: $37 + $4 per employee monthly
- Unlimited payroll, tax filings, year-end tax reporting, multiple pay rates and schedules, PTO accruals, and free two-day direct deposits for qualified clients
Basic: $17 + $4 per employee monthly
- Full service plan but without tax filing services—you handle tax payments and filings yourself
Add-on fees
- Multistate tax filings: $12 monthly for each additional state
- 1099 e-filings (for Basic Payroll subscribers only): $20 for up to five 1099 e-filings; an additional $2 per 1099 is required for six to 35 filings (no additional charge for 36 or more)
- HR software: Starts at $6 + $2 per employee monthly; includes employee data management and reporting tools
- Time and attendance: Starts at $6 + $2 per employee monthly
- Accounting software: Starts at $20 per month (can be purchased as a standalone solution)
Patriot Payroll made it on our list of best payroll software for accountants because of its reasonably priced plans, solid payroll and accounting tools, and competitive discount offers for partner accountants. It also comes with time tracking and basic HR solutions for monitoring staff work hours, creating overtime rules, and managing an online employee database. While these tools are paid add-ons, adding both to Patriot’s payroll platform makes it ideal for your clients who employ mostly hourly workers and want to accurately capture employee attendance.
In our evaluation, Patriot Payroll earned 4.18 out of 5, with perfect marks in reporting, pricing, and popularity among users. It also received high scores in accountant-specific and pay processing tools, given its helpful client dashboard, seamless integration with its accounting software, including QuickBooks, and the ease of running payroll with Patriot. It scored the lowest in HR features because it lacks onboarding, state new hire reporting, and benefits options.
Patriot Payroll’s client dashboard lets you switch between company accounts easily. (Source: Patriot Payroll)
Patriot Payroll Overview
If you want to understand its features more, including the pros and cons of using the system, read our Patriot Payroll review.
Paychex: Best Payroll Software for Accountants Looking for Continuing Education Perks
Overall Score:
4.09 / 5
Pros
- Full suite of HR tools
- Full-featured payroll options
- Continuing education through Paychex’s online courses and Accountant Knowledge Center
Cons
- Pricing isn’t all transparent
- Time tracking is a paid add-on
- Payroll tax administration and year-end reporting cost extra
Paychex Flex Pricing
Paychex Flex Essentials: $39 + plus $5 per employee
- Includes full-service payroll, payroll tax administration with year-end tax reporting*, workers’ compensation, new hire reporting, direct deposit option, self-service portal, and garnishment payment services
Paychex Flex Select: Custom priced
- Essentials (except garnishment payment services) + dedicated payroll specialist, time tracking*, and learning management
Paychex Flex Pro: Custom priced
- Select + garnishment payment services, accounting software integration, onboarding and background screening
*Additional fees may apply
Paychex’s payroll and HR software for accounting professionals offers technology and partnerships that help you provide excellent service for your clients. It starts with a client dashboard, called AccountantHQ, where you can work with clients to run payroll (through its Paychex Flex solution) or run it yourself. Next, it adds HR tools like onboarding, new hire reporting, background checks, and hiring services. On top of that, it includes access to professional education webinars, compliance support, resources and tools to help improve client relationships, and a dedicated account services team of accountant relationship managers.
Since Our Last Update:
The provider has released its “Paychex Voice Assist” feature, which offers a hands-off experience in processing, reviewing, updating, and submitting payroll. This voice-activated tool, which works on any Google Assistant-compatible device, comes with built-in verification and artificial intelligence (AI) solutions for user authentication. You can start a new pay period, make adjustments, or continue a pay run that’s already in progress—without having to manually log into your Paychex Flex account.
In our evaluation, Paychex earned an overall of 4.09 out of 5. It scored the lowest in pricing because most of its HR and payroll products require you to call for a quote. Nonetheless, it offers a terrific range of payroll and tax filing services, including a dedicated payroll specialist. You can offer clients HR support, given Paychex’s wide selection of online tools—from hiring and employee benefits to learning management and even PEO services.
Paychex’s AccountantHQ solution provides you real-time access to your clients’ payroll and HR information. (Source: Paychex)
Paychex Overview
Read our Paychex Flex review if you want to find more to like about this cloud-based system.
SurePayroll: Best Affordable Solution for Accountants Needing Simple Payroll Tools
Overall Score:
4.03 / 5
Pros
- Unlimited and automatic pay runs
- Revenue share or direct billing options
- Offers an online branded client portal
Cons
- Free payroll software perk is only available to those with at least 10 clients
- Doesn’t provide continuing education perks
- Revenue sharing has a monthly add-on fee
- Limited HR tools
SurePayroll Pricing
Full-Service: $29.99 + $5 per employee monthly:
- Includes unlimited pay runs, payroll tax filings, year-end tax reporting, two-day direct deposits, online pay stubs, and new hire reporting
No Tax Filing: $19.99 + $4 per employee monthly:
- Full-service plan but without payroll tax filing services—you have to handle this yourself
Add-ons
- Ohio and/or Pennsylvania local tax filing services: $9.99 per month
- Multiple state filings: $9.99 per month
- Time clock integration: $9.99 per month
- Accounting integration: $4.99 per month
SurePayroll is a Paychex company and offers many of the same services, but it’s a simpler and less expensive software. In addition to full-service payroll, tax filings, basic HR tools, and access to benefits options, it offers a partner program for accountants with a platform for managing clients, dedicated support, and wholesale pricing. It also provides white-label branding features, such as you can customize its client portal. For an additional fee, you can use its Revenue Share option to manage client billings. This allows you to set specific markup fees for each client and send them invoices.
In our evaluation, SurePayroll received an overall rating of 4.03 out of 5, earning high marks of 4 and above in pricing, payroll functionalities, and reporting. While it offers efficient payroll and accountant tools and has mostly positive feedback on online review sites, it scored the lowest in popularity among users since its average number of reviews on third-party sites is below 500.
A snapshot of SurePayroll’s client dashboard for partner accountants (Source: SurePayroll)
SurePayroll Overview
Read our SurePayroll review to learn more about the platform’s pay processing tools.
How We Evaluated the Best Payroll Software for Accountants
The first thing we looked for is payroll software with partner programs specific to accountants. The software also needed to provide more than discounted pricing, so we checked for client dashboards and benefits specific for accountants. Then, we compared essential features, such as pay runs, tax filings, and HR tools. Finally, we considered the price for clients and accountants.
Click through the tabs below for a more detailed breakdown of our evaluation criteria.
20%
Pricing
20%
Accountant-specific Tools
15%
Payroll Features
15%
Expert review
10%
HR features
10%
Ease of Use
5%
Popularity
5%
Reporting
20% of Overall Score
20% of Overall Score
We looked for payroll software with partner accountant programs, discounted pricing for both clients and accountants, and a client portal. We also considered whether it has an in-house accounting solution or integrates with popular accounting software.
15% of Overall Score
We gave priority to software that has two-day direct deposit, handles all payroll tax payments and filings, and provides a penalty-free guarantee.
15% of Overall Score
In this criterion, we assess whether the software’s ease of use, pricing, and the width and depth of its payroll and HR tools are ideal for SMBs.
10% of Overall Score
Access to expert support, including online onboarding and state new hire reporting, are the top HR features we looked for, followed by benefits options, health insurance available across the US, and a self-service portal.
10% of Overall Score
Payroll service and software should be simple to set up, be customizable, and have a user-friendly interface. We also looked at whether the provider offers live support and integration options with online tools that most SMBs use.
5% of Overall Score
We considered user reviews, including those of our competitors, based on a 5-star scale; any option with an average of 4-plus stars is ideal. Also, any software with 1,000-plus reviews on any third-party site is preferred.
5% of Overall Score
Preference was given to software with built-in basic payroll reports and customization options.
*Percentages of overall score
If you just want to recommend payroll software to your clients, then check out our guides on the best payroll software and leading payroll services.
Best Payroll Software for Accountants Frequently Asked Questions (FAQs)
Apart from accounting software (like QuickBooks Online or Xero), accountants may use a payroll system (such as the payroll software mentioned in this guide) for processing their clients’ pay runs and tax filings. Some may also use expense management, invoicing, and billing solutions—if those functionalities aren’t included in the accounting software.
Pricing can vary, depending on the features included. An accountant payroll software with basic pay processing tools can cost anywhere from $40–$50 monthly for one employee. Those with advanced HR payroll tools are priced at around $80 to $100+ for one employee monthly.
For accountants or accounting firms, it’s important to find an online system that can handle the payroll needs of your clients—from simple pay runs to processing multi-state payroll. Consider the integration options offered and the HR tools included (such as time tracking, new hire reporting, and onboarding), as these can help streamline processes.
Also, look at customer support and whether the payroll accounting software has an intuitive and user-friendly interface. Pricing is another important feature, so be sure to look for providers that offer unlimited payroll (so you don’t have to pay extra for each pay run) and reasonably-priced plans with discounts for partner accountants.
Bottom Line
Finding payroll software that also offers an accounting solution is critical if you’re offering payroll accounting services. It makes bookkeeping easy and doesn’t require you to input payroll-related data manually into your books since its accounting and payroll tools integrate seamlessly with each other. If you have preferred accounting software, check if it offers payroll and vice-versa. Then, consider the needs of your clients and add-on solutions that would be helpful to you and your customers, such as basic HR and benefits options.
We find QuickBooks Payroll is the best payroll software for accountants managing small businesses because you can use its integrated payroll and accounting platform to transfer payroll data to the general ledger, saving you time from doing it yourself. It also offers free payroll for your company, a client dashboard, a revenue share option, and discounted rates for you and your clients.
