7 Best Payroll Software for Accountants

Your clients can choose from three plans:

• Payroll Core: $50 base fee + $6 per employee monthly
  • Includes full-service payroll, next-day direct deposit, federal and state tax filings, and access to 401(k) plans and benefits
• Payroll Premium: $85 base fee + $9 per employee monthly
  • Core + same-day direct deposit, tax filings in all levels, time tracking, workers’ comp administration, and HR support center
• Payroll Elite: $130 base fee + $11 per employee monthly
  • Premium + project tracking, personal HR advisor, expert setup, and tax penalty protection up to $25,000 per year

QuickBooks also offers a package for paying contractors. However, this plan is available to small businesses that only pay 1099 workers.

• 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

If you want to enjoy an ongoing ProAdvisor discount, you can choose to pay your clients’ monthly payroll software fees. You can also pass the discount to new customers through a Direct Discount option, but only for the first 12 months. QuickBooks will even send the billings directly to your clients, so you don’t have to worry about preparing this.

QuickBooks Payroll also has a revenue share program, wherein partner accounting firms or accountants—except those offering audit services—get a monthly payout for new client subscriptions (30% from base fees and 15% from per-worker fees). However, you can only collect the monthly payouts or revenue shares during your clients’ first 12 months of using QuickBooks Payroll via your firm. It even lets you pass along a client discount of 50% to new customers for their first three months (plus, they get one month of free payroll).

Note that local tax filing and payment services aren’t available in the Core package. You have to convince your clients to sign up for at least a Premium plan if they want tax filing services at all levels (federal, state, and local). And, while you get preferential pricing under the ProAdvisor program, its discounted Premium tier ($56 plus $6.80 per employee monthly) is still pricier than Patriot Payroll, which offers full-service payroll and automated tax filings for only $37 plus $4 per employee monthly.

As a partner, you get a free QuickBooks Online Accountant solution where you can access your clients’ QuickBooks accounts to check their books, edit transactions, and address payroll issues. These functionalities make managing both client payroll and bookkeeping easy for accountants. Apart from the ProAdvisor and client discounts, its partner program comes with training and certification programs to help improve your skills and grow your accounting business.

You can enroll in free QuickBooks Online Certification training programs to gain expertise in Intuit QuickBooks products like payroll and accounting. (Source: Intuit QuickBooks)

• Pay contractors, hourly workers, and salaried employees with just a few clicks.
• Payroll runs are unlimited and automatic, with salary payouts made through paychecks and via next-day and same-day direct deposits.
• On-the-go business owners can process payroll via the mobile web browsers of smartphones and tablets.
• Users are covered by a tax accuracy guarantee, where the provider will handle all tax filing penalties if its representatives are at fault. However, Elite plan holders also get a tax penalty guarantee, where QuickBooks will cover penalties of up to $25,000 per year—regardless of who made the tax filing error. The other accountants payroll software in this guide only offer a tax accuracy guarantee.
• In addition to pay-as-you-go workers’ compensation (via Next) and 401(k) plans (via Guideline), you are granted access to health insurance (via Allstate Health Solutions) that’s available in all states. This is unlike Patriot Payroll, which doesn’t offer benefits plans, and Gusto’s health benefits, which only cover 38 states and Washington, D.C.

Gusto offers three plans:

• Simple: $49 per month + $6 per person per month
  • 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 base fee + $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: Call for a quote
  • 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

Similar to QuickBooks Payroll, it has a special package for small companies that only pay contract workers.

• Contractor-only plan: $35 base fee + $6 per contractor monthly
  • Full-service payroll, four-day direct deposits, and state new hire reporting

Add-on solutions and services

• State payroll tax registration: Pricing varies per state
• International contractor payments: Pricing varies
• R&D tax credits: 15% of identified tax credits
• HR advisory services for Plus plan only: $8 per employee monthly (this is included for free in the Premium tier)
• Health and other benefits: Pricing varies by benefit
• Gusto Global: $699 per employee monthly
  • Employer of record (EOR) solution for global recruiting and employee pay processing

When signing up for Gusto’s partner accountant program, you will be asked to choose one of its discount and incentive options:

• Gusto to bill your clients at discounted rates
• Gusto to bill your clients using advertised rates, but you’ll receive revenue shares
• Gusto to bill you at a discounted rate

The percentage of the discount or revenue share varies depending on the number of clients you have. Newly enrolled accountant partners are also required to run client payroll with Gusto within 30 days of signing up for the program to receive the resulting discount or revenue share.

Partner accountants get several perks, such as free payroll migration for your clients and free payroll software for your firm (provided you enroll one client with Gusto per year). You also get the chance to be People Advisory Certified and featured in the Gusto Partner Directory.

You need to have at least three clients with Gusto to enjoy discount perks. If you want to get preferential rates or plan to pass discounts to your customers without having to follow client limits, consider QuickBooks Payroll. Its ProAdvisor program offers the same discounts—30% and 15% off the monthly base and per-employee fees, respectively—regardless of the number of clients you have.

With its client dashboard, Gusto Pro, you can manage your customers’ payroll needs, track pay run deadlines, and spot issues like missed and blocked payrolls. It also includes access to helpful resources on maintaining revenue and regulatory changes, enabling you to provide personalized guidance to your clients.

All accountant partners get free Gusto marketing collateral, cobranded dashboards, and referral tools to help advertise payroll services to clients. As your client base grows, you get additional marketing resources—like inclusion in Gusto’s partner directory, Gusto partner badges you can add to your website, and a featured partner profile.

Gusto Pro’s analytics tool allows you to get the data and client payroll trends you need to manage customer accounts. (Source: Gusto)

• Unlike QuickBooks Payroll, all of Gusto’s plans include tax payment and filing services for federal, state, and local taxes. It also handles tax filings and year-end tax reporting.
• Gusto helps you manage time tracking, new hire reporting, onboarding, and workforce costing. It even has job posting tools to help you advertise open jobs, as well as a performance management solution for assessing your employees’ performance at work.
• Expert HR advisers are available, including an HR library that contains job description templates, sample policies, and HR guides.
• While its health insurance is available only in 38 states and Washington, D.C., Gusto offers a wide range of benefits options like pay-as-you-go workers’ comp, health reimbursement, 401(k), life and disability plans, health savings accounts (HSAs), flexible spending accounts (FSAs), and Dependent care FSAs.
• Gusto’s free financial management app, Gusto Wallet, has time tracking capabilities and a paycheck splitter option if you want to automatically transfer a portion of your payroll funds to a separate account as savings.
• EOR service helps you hire and pay global employees, while its international contractor payments allow you to pay contract workers in over 120 countries.

Unlike the other accountant payroll software in this guide, OnPay only offers one payroll plan. For a monthly fee of $49 plus $6 per employee, you are granted access to all of its payroll and HR features. Rippling may have a similar pricing scheme, but it lets you customize your package based on the HR, payroll, IT, and finance tools you need.

OnPay’s partner accountant perks include free account setup and data migration, marketing resources, free payroll for your firm, and options for either discount or revenue sharing. You can also pass the discount to your clients and have OnPay send billing statements to their offices. The incentives are based on the number of clients you have.

You get free integration setup with QuickBooks or Xero, making it easy for you to sync payroll data with these accounting solutions. OnPay even offers custom item mapping setup with both software to help you create accurate general ledger entries. And, while you can choose to keep payroll processing control to yourself, OnPay’s six-level permission settings allow you to delegate payroll tasks to someone else from your firm or hand them off to clients.

OnPay allows you to assign other accountants in your firm to access and manage the payroll customer accounts of specific clients. (Source: OnPay)

• OnPay offers unlimited pay runs, multiple pay rates and schedules, and multistate payrolls.
• Pay employees through checks, debit cards, and direct deposits. Note that you have to undergo OnPay’s risk assessment to identify whether you’re eligible for two- or four-day direct deposits. For fast direct deposits without the risk assessment, we recommend QuickBooks Payroll—it has next-day and same-day options.
• HR tools include employee onboarding, paid time off (PTO) management with in-app requests and approvals, offer letters, and state new hire reporting.
• Has built-in document templates, compliance alerts, online document storage, and an HR resource library.
• OnPay provides health insurance in all 50 states (unlike Gusto’s health plans, which only cover 38 states). Other benefits include disability, life, and retirement plans.

SurePayroll offers two plans, but to manage client payroll, consider getting the Full-Service option, as it includes tax filing services.

• Full-Service: $39 base fee + $7 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: $20 base fee + $4 per employee monthly
  • Full-service plan but without payroll tax filing services—you have to handle this yourself

Add-on services and solutions

• 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’s partner accountant program includes free account setup, dedicated support, and free access to its payroll tool you can use for your firm—provided you have 10 clients. It comes with a white-label option to help boost brand exposure and your firm’s payroll services. Flexible billing options are also available.

• Direct billing: SurePayroll by Paychex will bill you its software costs, allowing you to set a markup rate when invoicing clients for payroll services.
• Revenue share billing: For an additional fee, SurePayroll by Paychex lets you handle all customer billing through its software. You can even specify markup rates for payroll services on a per-client basis.

SurePayroll is the only payroll software for accountants we reviewed that charges extra for revenue sharing. With Gusto, QuickBooks Payroll, and OnPay, you only have to sign up for its partner accountant program and either select revenue sharing as your incentive or earn dividends.

With SurePayroll, you get white-label branding tools so you can customize its client portal to match your company’s color scheme. It may not have an accounting solution like QuickBooks and Patriot, but its platform can connect with accounting software like Xero, Zoho Books, LessAccounting, Kashoo, QuickBooks, Sage 50, and AccountEdge. Aside from a client dashboard, you are granted free access to a library of marketing resources and case studies to help you grow your accounting practice.

A snapshot of SurePayroll’s client dashboard for partner accountants (Source: SurePayroll)

• SurePayroll offers unlimited pay runs each month with payout options that include paper checks and two-day direct deposits.
• Similar to Patriot Payroll, it offers a full-service pay processing package with tax filing services and a do-it-yourself (DIY) plan, which is optimal for clients with a very small team—provided you’re willing to handle tax payments and filings yourself.
• New hire screening tools include background checks, drug screening, behavioral assessments, and skills testing.
• Benefits offerings include health insurance, 401(k) plans, and workers’ compensation. However, if your clients are looking for a financial management tool, consider Gusto.

Justworks offers two PEO packages:

• PEO Basic: $59 per employee monthly
  • Includes full-service payroll, tax filings, contractor and vendor payments, expense reimbursements, PTO management, employee onboarding, basic timecards, customizable reporting, HR advisory services, and access to benefits plans
• PEO Plus: $109 per employee monthly
  • PEO Basic + advanced analytics, COBRA administration, and access to additional employee benefits, such as mental health resources and medical, dental, and vision plans

It also offers a standalone payroll tool, which costs $50 plus $8 per employee monthly, which doesn’t include vendor payments and employee benefits plans (but can calculate and apply benefits deductions).

Add-on services and solutions

• Justworks Time Tracking: $8 per employee monthly
• International contractor payments: $39 per worker monthly
• Employer of Record: $599 per employee monthly

Instead of getting discounts, you can earn referral bonuses of up to $300 per employee. If providing client discounts is more important, you can waive your referral bonus and offer new clients up to three months of free admin fees. Note, however, that these perks are based on the number of PEO clients you have.

With Justworks, you get a Partner Relationship Management tool to track and manage new referrals. Access to compliance resources, R&D tax credit assistance, and dedicated support are also available.

While its team of HR-certified professionals can help you navigate the complexities of managing compliances and employee issues, Justworks provides 24/7 support for you and your clients via Slack, phone, email, and chat.

• Automated and unlimited pay runs let you process payments for employees and contractors, including vendors (the other payroll software for accounting firms we reviewed only support employee and contractor payouts).
• HR tools integrated with its payroll module, allowing you to onboard/offboard workers and track employee attendance, including PTO.
• Select the best plan from a wide variety of standard and non-standard employee benefits options to help you attract and retain employees.
• Non-standard benefits include options to help employees manage mental health and financial resources. It also provides teleconsultation services (via One Medical and where available) and support for gynecological, fertility, and family-building (e.g., adoption and surrogacy) issues.
• Expert support with 24/7 access; plus, Justworks touts a 45-second average wait time for phone support and a customer satisfaction score of 4.8 out of 5.

While Rippling’s pricing page indicated that its monthly fees start at $8 per user, you have to call the provider to get a quote. It will work with you to build an HR payroll package with the solutions and services that your business needs.

In the quote we received, Rippling’s core platform with payroll, time tracking, onboarding/offboarding, and integration tools is priced at $35 plus $8 per employee monthly. Adding IT tools to manage apps and computer devices to its platform will cost you an additional per-employee of $8 monthly.

Here are some of its custom-priced add-on products:

• Recruiting
• Benefits administration
• Learning management
• PEO services
• EOR services
• Expense management
• Corporate cards

Rippling’s partner program provides accountants free access to payroll and HR solutions that you can use for your firm. You even get a dedicated partner success manager and partner enablement materials, so you can become a better payroll adviser to your clients.

For your new customers, it offers free white-glove payroll migrations to help your clients easily transition from their current payroll system to Rippling. Your clients can also enjoy discounts of up to 35%. However, if you want training perks, consider QuickBooks Payroll and Paychex since both include learning courses in their partner programs.

Unlike QuickBooks and Patriot, Rippling lacks an in-house accounting tool—although it can integrate with QuickBooks, Sage Intacct, and Xero. Keeping track of all of your customers’ payroll needs and timelines is also made easy with Rippling’s client command center. Plus, it assigns all partner accountants with a dedicated Rippling Advisor who will serve as their point person if they have inquiries about the platform’s features, the program’s marketing tools, and more.

With the online accountant partner directory, you can create a listing for your firm and market your services to Rippling customers. (Source: Rippling)

• Unlimited pay runs and auto-calculations of pay rates are just some of Rippling’s payroll features. You can pay both employees and contractors either through paychecks or direct deposits.
• Rippling flags errors and pay data discrepancies between your draft pay runs and processed payrolls.
• With Rippling, you only need to enter data once, and its software will automatically reflect the changes across its HR, IT, payroll, and expense management solutions. You also don’t have to worry about having to do employee attendance data uploads because its time tracking tool connects seamlessly with its payroll solution, making it easy for you to capture the actual hours worked for pay processing.
• Rippling makes assigning and deploying computer devices to new hires easy. You can even install the necessary apps on computer devices and restrict access for resigning employees.
• Rippling can connect with more than 500 business apps. None of the providers on this list have a partner network this extensive.

Patriot has two payroll plans: Basic and Full Service. Between the two plans, you should offer the Full Service option to your clients as this comes with tax payment and filing services. With the Basic plan, you may need to handle your customers’ tax filings yourself.

• Full Service: $37 base fee + $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 base fee + $4 per employee monthly
  • Full service plan but without tax filing services

Add-on solutions and services

• Multistate tax filings: $12 monthly for each additional state
• 1099 e-filings (for Basic 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 base fee + $2 per employee monthly
• Accounting software: Can be purchased as a standalone tool or as an add-on solution
  • $20 monthly for the Basic accounting package
  • $30 monthly for the Premium package, which includes additional invoicing and account reconciliation features

Accounting firms that join Patriot Payroll’s partner program enjoy discounted rates based on the number of clients they have. For companies with up to 100 clients, discounts range anywhere from 5% to 20% for its payroll and accounting modules. Bigger discounts are available for those with 100 and more employees. And unlike Gusto and OnPay’s discount perks, which require at least three customers—with Patriot, you get 5% off even if you only have one client.

While you can’t pass the discount to your customers, paying Patriot Payroll’s subscription fees on behalf of your clients lets you set your own price for your services—regardless of the discount you enjoy. And if your clients require multi-state payroll, Patriot will only charge you $10 per additional state for payroll tax filings (instead of $12 per additional state). You can even use its payroll and accounting software for your firm at no cost, provided you have six or more active clients.

With Patriot Payroll’s client dashboard, you can add and manage your customers’ payroll information with ease. A cobranding service is also available, where your firm’s branding will appear throughout its software. While it offers accounting software integration with QuickBooks Desktop and QuickBooks Online, Patriot has its own accounting solution that you can purchase for either $20 or $30 per month.

Patriot’s onboarding dashboard lets you monitor your client onboarding activities online. (Source: Patriot Payroll)

• Pay hourly and salaried employees with ease, including contractors. In addition to unlimited payroll, you can also set its system to run automatically—provided you have already processed a successful payroll and don’t expect any changes to it.
• In case your clients want to give employee bonuses, simply add the expected take-home amounts into Patriot, and its “Net to Gross Payroll” tool will automatically gross it up for taxes.
• Patriot allows you to change employee hourly pay rates while processing payroll without leaving the page or canceling the pay run. This helps you save time from having to switch between its payroll tool and employee database.