Finding payroll software that can help you manage employee and contractor payments can sometimes be challenging. If you’re on the hunt for the best payroll services for nonprofits, look for a provider that offers budget-friendly solutions with essential features, such as tax filing and quick payment options. The provider should also understand your needs as a nonprofit and streamline payroll processes so you can focus more on running your organization.
To find the optimal nonprofit payroll software, we evaluated 13 solutions and narrowed the list down to our top five recommendations.
- Gusto: Best overall nonprofit payroll software
- QuickBooks Workforce (formerly QuickBooks Payroll): Best for QuickBooks accounting users
- OnPay: Best for payroll compliance and delegating payroll tasks
- Rippling: Best for HR and payroll automation
- Patriot Payroll: Best for small nonprofits with simple pay processing needs
- Payroll Software for Nonprofits Compared
- Gusto: Best Overall Payroll Software for Nonprofits
- QuickBooks Workforce: Best for QuickBooks Accounting Users
- OnPay: Best for Payroll Compliance & Delegating Payroll Tasks
- Rippling: Best for HR and Payroll Automation
- Patriot Payroll: Best for Small Nonprofits Needing a Simple Payroll Solution
- How to Choose the Best Payroll Software for Nonprofits
- Nonprofit Payroll Frequently Asked Questions (FAQs)
- Bottom Line
Payroll Software for Nonprofits Compared
All the pay processing software we reviewed offer full-service payroll with tax filing services and access to year-end tax reports. Paid time off (PTO) tracking features are also available, including basic employee information management tools. Below are each of the providers’ pricing and key functionalities.
| Special Promotion for New Clients | Starter Monthly Pricing | Contractor-only Payroll Plan | Nonprofit Features | |
|---|---|---|---|---|
 | One month free | $49 per month + $6 per person per month | $6 per worker + $35 monthly | Charitable donations, Aplos and MonkeyPod integrations |
| Visit Gusto or Jump to Section ↓ | ||||
 | 30 days free trial or 50% off base fees for three months | $50 per month + $6.50 per employee monthly | $15 for 20 contractors; plus $2 for each additional worker | QuickBooks accounting for nonprofits |
| Visit QuickBooks Workforce or Jump to Section ↓ | ||||
 | First month is free | $6 per employee + $49 base fee | ✕ | Expert handling of FUTA exemptions for nonprofits |
| Visit OnPay or Jump to Section ↓ | ||||
 | First month is free | $8 per employee + $35 base fee | ✕ | Payroll compliance, Bright Funds integration |
| Visit Rippling or Jump to Section ↓ | ||||
 | 30 days free trial | $4 per employee + $37 base fee | ✕ | Experience with churches and small nonprofits |
| Visit Patriot Payroll or Jump to Section ↓ | ||||
Looking for something more robust? Consider a professional employer organization (PEO) service like Justworks. It covers everything from hiring to retiring, handles payroll in multiple states, assumes tax liability, and generally takes HR worries off your hands. It’s No. 1 on our list of best PEOs for small businesses and, at $79 per employee monthly, is an affordable option. Plus, it offers discounts to nonprofits.
Gusto: Best Overall Payroll Software for Nonprofits
What We Like
Gusto’s excellent tools earned it first place in our guides to the best small business payroll software and the best payroll services. Its price point, ease of use, and integration with nonprofit management software earn it the top spot on this list as well. Its contractor-only payroll plan is a good option if you only work with contract employees. Gusto offers excellent tools for employees too, including Gusto Wallet, which makes it easy to budget, save, and even give to charities.
In our evaluation, Gusto earned an overall score of 4.45 out of 5. It earned high ratings in nearly all our criteria, with perfect marks for popularity and reporting. While Gusto doesn’t currently offer health insurance in all 50 states like OnPay and Rippling, it’s reasonably priced, easy to use, and highly regarded by users.
Users love Gusto’s easy interface. (Source: Gusto)
Gusto Plans
- Simple: $49 per month + $6 per person per month
- Plus: $80 per month plus $12 per employee monthly
- Premium: Contact sales
- Contractor-only payroll package: $35 plus $6 per contractor monthly
Add-ons
- State payroll tax registration: Pricing varies per state
- International contractor payments across 120-plus countries: Custom-priced
- Health insurance and other benefits: Pricing varies by benefit
- HR advisory services for Plus plan only: $8 per employee monthly; included for free in the Premium tier
*NOTE: Get one month free when you run your first payroll. Offer will be applied to your Gusto invoice(s) while all applicable terms and conditions are met or fulfilled.
- Nonprofit functionalities: Gusto makes it easy to set your Federal Unemployment Tax Act (FUTA) exemption (the others on our list also do this). It integrates with Aplos and MonkeyPod, online solutions for managing nonprofits and donations. Its Gusto Giving feature also allows employees to make donations straight from their paychecks and lets you match them. Gusto reports these contributions automatically in Box 14 of the IRS Form W-2. None of the payroll software for nonprofit organizations we reviewed offer a similar feature.
- Employee benefits: Gusto can broker with 30 carriers for more than 9,000 benefit plans, including health insurance, 401(k)s, FSAs, commuter benefits, and more. However, Gusto’s health insurance is unavailable in Alabama, Alaska, Hawaii, Louisiana, Mississippi, Montana, Nebraska, North Dakota, Rhode Island, South Dakota, West Virginia, and Wyoming.
- Financial benefits: Its free Gusto Wallet app provides access to a debit card and lets employees create budgets, set savings goals, and split paychecks among multiple accounts.
- Third-party software integrations: Gusto’s software integration options include FreshBooks, Xero, QuickBooks, When I Work, Homebase, and Expensify. This flexibility is a huge plus for Gusto. Patriot, for example, only integrates with its own accounting software and QuickBooks.
If you want fast payments, Gusto offers a next-day option if you subscribe to its higher tiers. But if you’re not keen on upgrading your plan, consider QuickBooks Workforce. It offers next-day direct deposits in all of its plans and same-day direct deposits in premium ones.
QuickBooks Workforce is also a good option if you’re looking for nonprofit payroll services to process only contractor payments. Its contractor plan is even more affordable than Gusto’s ($15 for 20 contractors plus $2 for each additional worker vs $35 plus $6 per worker).
QuickBooks Workforce: Best for QuickBooks Accounting Users
What We Like
QuickBooks Workforce nabbed the second spot on our list of best payroll services for nonprofits because of its fast payouts and reasonably-priced plans. With its payroll function easily accessible through the QuickBooks system, it saves QuickBooks users time from having to separately set up a chart of accounts and import pay-related data into its platform. The seamless connection between Intuit products is a huge competitive advantage, especially to those with very limited integration capabilities, such as Patriot Payroll.
With an overall score of 4.24 out of 5 in our evaluation, QuickBooks Workforce earned high ratings in nearly all of our criteria. It lost points for not having a pay card option and integrations with nonprofit management software. User popularity ratings were good but not as high as the others on our list. Overall, real-world users liked the software for ease of use—but said that its setup could take some time, and the support could be problematic at times.
QuickBooks lets you pay with direct deposit or print your own checks. (Source: QuickBooks)
QuickBooks Workforce Plans
- Workforce Payroll: $50 per month + $6.50 per employee monthly
- Workforce Premium: $88 per month + $10 per employee monthly
- Workforce Elite: $134 per month + $12 per employee monthly
- Contractor payments package: $15 monthly for 20 workers; plus $2 for each additional contractor
For help deciding which payroll package is best for you, check out our QuickBooks Workforce plans comparison.
- Nonprofit functionalities: QuickBooks Workforce lets you set up your FUTA exemption easily. If you use QuickBooks Accounting, it has a feature for nonprofits that can help manage donations and track how money is spent for fundraising programs. You can integrate this with other payroll software on our list, but it’s seamless with QuickBooks Workforce.
- Flexible direct deposits: QuickBooks Workforce offers next-day deposits for its Core subscribers and same-day direct deposits for Premium and Elite plan holders. The quickest direct deposit speed that most of the nonprofit payroll services on our list can offer is next-day funding, so same-day payments are a huge value add for QuickBooks Workforce.
- Tax penalty protection: Similar to the other nonprofit payroll software we reviewed, QuickBooks will cover all tax penalties, but only for its own filing mistakes. With its Elite plan, QuickBooks will cover the penalty and interest for any payroll tax error for up to $25,000 a year—regardless of who made the error.
While QuickBooks Workforce has an online wizard to guide you through the setup process, it only offers its setup services to Elite plan holders. We recommend Patriot Payroll, as it can help create your account and add employee data into its system for free.
QuickBooks Workforce also only has a handful of HR solutions for managing the entire employee lifecycle. For a robust HR payroll system, try Rippling. It has a wide suite of HR solutions—from hiring and time tracking to learning management and compensation planning.
OnPay: Best for Payroll Compliance & Delegating Payroll Tasks
What We Like
OnPay makes it easy for nonprofit organizations to onboard new hires and pay different types of workers—from employees to contractors and volunteers. It can handle multiple pay rates, ensures compliance with county and other local jurisdiction tax rules, and automatically withholds the applicable federal and state taxes, including federal insurance contribution act (FICA) taxes. And, with its six levels of system permissions, you can choose who has visibility into payroll and HR, allowing you to securely delegate pay processing tasks.
In our evaluation, OnPay earned an overall score of 4.19 out of 5. Its ease of use, efficient HR tools, reasonably priced plan, and solid reporting functionality contributed to its high scores. However, its risk assessment to determine two- and four-day direct deposits cost it some points. And, while OnPay is highly rated on third-party review sites like G2 and Capterra, with reviewers liking its user-friendly platform, it received a low score in our popularity criterion because its average number of reviews on those websites is below 1,000.
OnPay automatically alerts you of pay errors during payroll runs. (Source: OnPay)
Most of the providers on our list of best payroll services for nonprofits offer multiple payroll packages, but OnPay only has one plan. For a monthly fee of $49 plus $6 per employee, you are granted access to all of its payroll, HR, onboarding, and benefits solutions.
- Nonprofit functionalities: You get automated state and federal taxes, including the expert handling of FUTA exemptions for nonprofits and charitable organizations. If you receive grant funding, OnPay can help you separate employee pay by grant items.
- Payroll support: OnPay lets you process payroll as many times as you want and with only a few clicks. If you need support, the provider has a team of payroll experts you can contact from Mondays to Fridays, either through phone, chat, or email. Weekend support is also available, but only through email and for emergency cases only.
- Employee benefits: Gusto’s health insurance coverage may be limited, but OnPay’s health plans are available in all 50 states. It grants access to most major providers (such as Aetna, United Healthcare, and Humana). Plus, you can easily generate employee census data reports, which you can use to get accurate benefits and health insurance quotes for your business.
You won’t be able to choose your direct deposit payout timelines with OnPay. The eligibility for either a two- or four-day direct deposit is based on the provider’s assessment. For direct deposit payouts without assessment requirements, we recommend Gusto. Two-day payouts are available in its basic plan, with a next-day option in higher tiers.
For a robust HR system, Rippling is a better option than OnPay. Its HR solution suite can manage a wider range of HR processes—from hiring to learning management and even compensation planning. Rippling’s functionalities extend to more than HR. It can handle expense reimbursements, manage business software access, and track the issuance of computers assigned to employees.
Rippling: Best for HR and Payroll Automation
What We Like
Rippling takes the stress out of managing pay runs given its robust workflow and automation tools that sync all of your employee and HR data with payroll. You don’t have to manually input employee clock-ins/outs or benefits deductions—the system will capture and calculate these for you. Rippling is also equipped to handle a wide range of payroll services, from paying employees to processing contractor payouts. Its EOR services can even help you hire and pay global workers for your nonprofit.
Scoring 4.13 out of 5 in our evaluation, Rippling earned perfect ratings in reporting and user popularity. Its solid HR features, customizable pricing plan, and ease of use contributed to its high scores. However, it lost several points because of its paid HR advisory services, lack of paycard and pay-on-demand features, and the non-straightforward way of asking for phone support (this has to be scheduled via its chat representatives).
Rippling attests that it can run payroll in 90 seconds. (Source: Rippling)
Rippling works with you to create a custom plan with the features that your business needs. Monthly fees start at $8 per employee, per module. Note that you have to purchase its workforce management platform before getting any of its modules.
For a payroll platform with time tracking, software integrations, and onboarding/offboarding tools, we were quoted a monthly fee of $35 plus $8 per employee. Adding Rippling’s IT tools to manage business apps and computer devices costs $8 per employee, per module monthly. Benefits administration services are also available, but pricing varies depending on the insurance broker.
Here are some of its add-on solutions and services:
- Global payroll: $20 per employee or contractor monthly*
- EOR services: $599 per employee monthly*
- PEO services: Custom-priced
- HR help desk: Custom-priced
- ACA & COBRA administration: Custom-priced
- Expense management: Custom-priced
- Headcount planning: Custom-priced
- Learning management: Custom-priced
- Compensation bands planning: Custom-priced
- Applicant tracking: Custom-priced
*Pricing is based on a quote we received
- Nonprofit functionalities: Its platform integrates with Bright Funds, a solution that supports employee donations and workplace giving programs. Rippling also automates compliance tasks—from remitting and filing payroll taxes to managing ACA notices across 50 states.
- Employee onboarding: Rippling makes new hire onboarding easy. When new employees are added into its system, Rippling automatically adds them for upcoming pay runs, enrolls them in eligible benefits (e.g., time off or vacation leave), and provides them access to your business apps, such as Slack, Zoom, or Microsoft 365.
- Employee benefits and perks: Rippling provides access to health benefits, retirement plans, and workers’ compensation. Its integration with solutions like Giften and Goody also allows you to add meal perks and electronic gifts as rewards or benefits under your employee recognition program.
- Robust integration options: Rippling connects with more than 500 apps—from finance and office management systems to graphic design and collaboration software. So, if your nonprofit organization is tech-heavy, it’s highly likely that you can integrate the apps that you use with Rippling.
Rippling doesn’t have a support team you can directly contact through the phone. You have to chat with one of its representatives to set a schedule for the call. For a support team you can easily contact via phone, consider any of the providers in this guide. Gusto is also a great choice, especially if you require priority support with access to a direct phone line—provided you upgrade to its higher plan for this option (or pay $8 per employee monthly if you’re on the Plus plan).
If your nonprofit employs mostly contract workers, it may be best to partner with QuickBooks Workforce. Unlike Rippling, the provider offers a contractor payments plan, which only costs $15 monthly for 20 workers (+ $2 for each additional contractor monthly).
Patriot Payroll: Best for Small Nonprofits Needing a Simple Payroll Solution
What We Like
Patriot Payroll is the only payroll for nonprofit we reviewed that offers a full-service option and a more affordable DIY version for doing payroll. It’s also the simplest on our list, with just the most basic payroll tools. Even the HR add-on is for employee data tracking and HR reports, whereas Rippling offers more HR tools and Gusto comes with hiring and performance reviews. However, with budgeting being such an important aspect of nonprofit financials, it is a great option for those looking for an affordable solution.
In our evaluation, Patriot Payroll scored a 4.04 out of 5, gaining top points for its budget-friendly software and popularity among users. It lost points for its limited HR features and only offering a four-day direct deposit funding period (the two-day option is only for qualified companies). Many other providers on our guide, such as Gusto, offer two-day funding in their starter tiers.
Patriot has a clean, bright interface that allows some customizations. (Source: Patriot)
Patriot Payroll Plans
- Basic: $17 per month plus $4 per employee monthly
- Doesn’t include tax filing services
- Full Service: $37 per month plus $4 per employee monthly
Add-ons
- Time tracking: Starts at $6 per month plus $2 per employee
- HR software: Starts at $6 per month plus $2 per employee
- Basic employee data management and HR reports
- 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)
- Nonprofit functionalities: Like the others on our list, you can set FUTA settings for nonprofit; otherwise, Patriot lacks specific nonprofit tools. It does work with nonprofits, particularly church organizations, and offers help articles on nonprofit payroll and HR issues.
- Free payroll setup: Patriot’s team will request all relevant information and get everything up and running for you—at no extra cost. If you prefer to do it yourself, you can utilize its payroll startup wizard.
- Self-service plan: You can save the most money if you choose to file your payroll taxes on your own using Patriot’s Basic tier. We recommend this plan for organizations with fewer than 10 employees, and those only operating out of one state. Otherwise, a DIY approach can get very complicated when it comes to compliance.
- Payroll tools: Both the DIY and Full-service plans let you run unlimited payrolls. Multiple pay rates can also be added per employee, which is great if they work at different rates depending on grants. For paying workers’ compensation insurance premiums, it integrates with AP Intego, a popular workers’ comp company used by the others on our list too.
While Patriot’s DIY approach keeps the price affordable, it also means that the time tracking and employee data management features included in the pricing of other providers on our list are an additional cost for Patriot. Another drawback is that direct deposit is four days rather than two, unless you contact support about the expedited function. If you want fast direct deposits, QuickBooks Workforce offers next-day payments in its starter tier.
How We Evaluated the Top Payroll Services for Nonprofits
We compared several of the most popular providers, focusing on features that would be most valuable for nonprofit organizations. We looked for payroll providers that offer unlimited pay runs, flexible direct deposit schedules, seamless integrations with third-party software, and the availability of both basic and customized payroll reports. Click through the tabs below for a more detailed breakdown of our evaluation criteria.
Aside from affordability, we made sure to break down what’s included and what’s extra in pricing. We also looked for pricing transparency and unlimited pay runs, as well as checked whether the provider offers special pricing or discounts to nonprofits.
We evaluated the providers by many of the features that we think are the most valuable for nonprofits. Automatic payroll, quick direct deposits, full-service tax filings and payments (federal, state, and local), and contractor payments are just a few. We also checked if the provider offers a penalty-free guarantee, in the event that it makes a mistake when processing your payroll.
Having a payroll solution that’s easy to use is important for busy nonprofits, including quick problem resolution and access to live phone support. We made sure to keep third-party integrations in mind as seamless integrations between payroll and accounting are key for nonprofits.
The best payroll software for nonprofits includes basic HR tools, such as online onboarding, new hire reporting, and employee benefits. Self-service portals that allow your team to manage their information also hold a huge value.
We considered online user reviews, including those of our competitors like G2 and Capterra, based on a 5-star scale, wherein any option with an average of 4-plus stars is ideal. Also, software with 1,000 or more reviews on third-party sites is preferred.
Aside from having access to basic payroll summaries, users should be able to customize reports within the system. Reporting is especially important for nonprofits that need an easy way to determine their payroll costs.
How to Choose the Best Payroll Software for Nonprofits
In selecting the payroll software or payroll services for your nonprofit, consider the following factors:
- Features: Take stock of the features you need and prepare a payroll systems checklist so you don’t miss anything. Look for those that can handle multiple pay rates, direct deposit payments, automatic payroll and tax calculations, and tax filing services.
- Ease of use and scalability: The payroll system should be simple to set up, learn, and use. If you plan to grow into a large nonprofit organization, consider those that offer scalable payroll solutions that can handle the complex HR payroll processes that come with managing a large workforce.
- Budget: Don’t forget to consider your budget. The cost of payroll services varies depending on the provider and the features you want. Be ready to spend more if you want advanced tools like learning management, recruiting, or performance reviews.
- Compliance: Check if the provider has the expertise to handle the tax reporting and compliance requirements of nonprofit organizations. Plus, having access to tax payment and filing services can take the stress out of having to do this yourself.
- Support: 24/7 support is ideal, but if this isn’t available, look for those that provide live phone or chat support.
Nonprofit Payroll Frequently Asked Questions (FAQs)
Yes. Nonprofit organizations are exempt from federal unemployment taxes and, in some cases, state unemployment taxes. Be sure to check that your payroll software notes this to avoid adding undue expenses and complications.
Payroll service providers make it easy to pay employees, sometimes taking only minutes to complete a pay run. Plus, these providers offer automated checks to make sure you are error-free and in compliance with federal, state, and even local laws.
Yes. You must withhold federal, state, and local income taxes as well as FICA (Social Security and Medicare) taxes from all qualifying employees. The exception to this may be clergy, who are often considered self-employed for calculating FICA and, thus, you may not need to pay this on their behalf.
Yes, because minimum wage applies to all qualified employees. There are some exceptions. Check with the US Department of Labor (DOL) or your state for details. The minimum wage is currently $7.25 an hour or higher if your state or local municipality has its own rate.
Bottom Line
Whether you’re looking for a full-service payroll solution or a more DIY approach, it’s important you find a nonprofit payroll software with the features you need. Essential functionalities can range from quick direct deposits to compliance support. You also have to consider pricing and whether or not the nonprofit payroll service you’re considering meets your budget.
We found Gusto to be the best payroll software for nonprofits. It offers reasonably priced plans with a contractor-only package that’s optimal for organizations that mostly hire contract workers. Gusto is a crowd favorite among users given its user-friendly platform and solid payroll tools. Sign up for a plan today.
