I tested top nonprofit payroll platforms and found Gusto best overall, Paychex strongest for tax compliance, and Rippling the most flexible.
Nonprofit organizations play a unique and crucial role in society. But just like any company, 501(c)(3) organizations still need to pay their employees, calculate and remit payroll taxes, and budget for payroll costs.
For nonprofits, payroll software has to do more than pay employees and calculate taxes. It should help track labor costs, keep payroll records clean, and make it easier to prepare reports for grants, boards, audits, and donors. When payroll data is messy, it can make budgeting harder, create compliance risks, and add extra work for already lean teams.
For this guide, I compared popular nonprofit payroll software to help you find the right one for your organization. Here are my top picks:
Our rating: 4.6 out of 5
Gusto is one of the best payroll software services for small businesses, large corporations, and nonprofits alike. For one thing, the software is extremely accessible. Whether you have a lot of practice paying employees or your organization just hired its first W-2 employee, it won’t take you long to get the hang of processing payroll with Gusto.
Just how simple is Gusto for nonprofits? I’ve found that the only main thing you have to do is enter your employees’ pay information. From there, you can set payroll to run automatically. Gusto will pay your employees on a pre-set pay schedule via direct deposit, calculate and deduct payroll taxes, and remit those taxes to the government on your behalf.
Frankly, I find it hard to find nonprofit payroll software more convenient, intuitive, and user-friendly than Gusto. If you’re anxious about processing payroll accurately, Gusto is the perfect software to start with.
What makes Gusto stand out is how little payroll knowledge it assumes from the user. That matters for small nonprofits where payroll may sit with an executive director, office manager, bookkeeper, or finance lead who already wears several hats. The easier the system is to run correctly, the lower the risk of missed steps, delayed payments, or manual workarounds.
Plus, as one of the most popular payroll providers in the United States, Gusto syncs with nonprofit-friendly business software, including accounting programs and nonprofit-specific software like Aplos and MonkeyPod.
Our Gusto review can tell you more.
Gusto lists pricing for four of its plans online:
Gusto also has a wide range of products if you need employee benefits, faster payment options, and priority support, including global payroll and hiring tools. Visit its website to view pricing details.
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Our rating: 4 out of 5
Paychex is one of the top payroll providers worldwide. Based on my experience, its software has a higher learning curve than Gusto, but it’s also equipped with more customizable reports and a much bigger HR library.
Paychex Flex also gives you many options for paying your employees, including via direct deposit, paycard, paper checks, and on-demand payment apps.
Paychex’s nonprofit payroll software solution caters to small and midsize businesses as well as to nonprofits of all sizes. Its platform simplifies financial activities such as tracking donations, filing taxes, and recording expenditures for nonprofits.
In contrast to Gusto, which only issues compliance alerts with its highest-tier plan, Paychex keeps you on top of potential tax compliance issues with frequent alerts and useful reporting.
Our Paychex review can tell you more.
While Paychex lists its plan details on its website, you have to call the provider to get a quote. For non-profits, this quote-based model can be helpful if you need payroll, tax compliance support, and benefits in one package. Note, however, that some features are paid add-ons, such as time tracking, HR analytics, and talent management tools.
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SEE: Why Does My Business Need a Payroll Service? (TechRepublic)
Our rating: 4.3 out of 5
Rippling is a domestic and global HR and payroll platform for both for-profit and nonprofit organizations. From tax deductions, PTO, and 401(k) calculations to HSA or FSA deductions — along with filing payroll taxes across all 50 states and internationally — Rippling takes care of compliance activities for you.
Crucially for nonprofits, Rippling lets users customize dozens of prebuilt reports. From the payroll dashboards, you can see, analyze, and share these reports across different teams and departments for seamless decision-making.
Rippling comes with a minimalist, user-first design that offers nonprofits a payroll system they can set up and start using without difficulty.
Additionally, what I found unique about Rippling among the nonprofit payroll services on our list is that it’s modular. Organizations that use Rippling can build their own HR, payroll, IT, and financial plans from the ground up.
It’s easy to start off using Rippling payroll when yours is a small one- or two-employee organization, and it’s just as easy to scale up in features as your nonprofit expands to reach even more individuals.
Learn more by reading our Rippling review.
Similar to Paychex, you have to call Rippling to get a quote. The provider works with you to create a package that fits your payroll needs. However, it can become pricey as you add more modules or features.
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Our rating: 4.7 out of 5
In my experience, OnPay is at least as user-friendly as Gusto, if not more so. OnPay’s team of professionals will set up your payroll software for you at no cost, and the payroll company’s excellent customer service team is available at extended hours to ensure you can resolve any payroll problems quickly and easily.
OnPay has fewer fees and hidden costs than just about any nonprofit payroll service on our list.
You don’t pay extra for just about anything, including wage garnishment, W-2 and 1099 form generation, accounting software integration, and multi-state tax filing — all payroll features that most other services charge extra for.
OnPay brings the same low-cost, high-value mentality to its nonprofit features as well. For instance, unlike Paychex, which charges extra for federal and state unemployment tax administration, OnPay helps nonprofits manage FUTA exemptions for 501(c)(3) organizations at no extra charge.
Learn more by reading our OnPay review.
OnPay has just one payroll plan that costs $49 per month plus $6 per employee paid per month. Every organization that uses OnPay gets the same nonprofit payroll features. There are no hidden fees, and the only price difference is determined by the number of people you pay.
If you want to add more tools to manage paid time off, onboarding workflows, documents, and HR insights, OnPay has an HR add-on, which costs $15 per month plus $2 per employee monthly. It even comes with equipment and software provisioning tools, org chats, HR insights, and a searchable employee directory.
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Our rating: 4.7 out of 5
If affordability is your top payroll consideration, I can’t recommend SurePayroll highly enough.
Its self-service plan puts payroll taxes in your hands, meaning the software calculates payroll taxes, but you take responsibility for remitting those taxes to the federal and state governments. For just $10 more a month, SurePayroll will remit taxes on your behalf.
However, that recommendation comes with one important caveat: SurePayroll is best for nonprofits with straightforward pay processing needs. If your organization expects rapid growth, more complex reporting, or broader HR support, you may outgrow it faster than a more scalable platform like Gusto, Paychex, or Rippling.
Both SurePayroll’s self-service and full-service options are among the cheapest payroll plans on the market. That said, SurePayroll doesn’t sacrifice features and quality for the sake of price.
Using SurePayroll will ensure your employees can access top-notch benefits without requiring you to devote more of your budget than necessary to running payroll.
Our SurePayroll by Paychex review can tell you more.
SurePayroll has only two plans, which means it isn’t particularly scalable for growing organizations. However, it’s nearly impossible to beat SurePayroll by Paychex’s low monthly and per-payee fees:
You also have to pay extra for additional features, such as:
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Our rating: 4.2 out of 5
Justworks is one of the top PEO companies, or professional employer organizations, in the U.S. These co-employment companies partner with nonprofits and other organizations, taking care of their HR and payroll tasks and leaving them free to focus on their organization’s daily operations and overall mission.
Professional employer organizations aren’t right for every nonprofit, but you might find them useful if you’re spending more time dealing with hiring and payroll than you can afford.
While Justworks isn’t the only PEO that works with nonprofits, it’s one of the best thanks to its low per-employee starting price, transparent pricing, and fully automated payroll.
Our Justworks review can tell you more.
Unlike most PEOs, Justworks lists its prices upfront. It’s a good pick for nonprofits, which have unique financial transparency requirements and donor obligations:
While both plans include the same payroll features, only the Plus plan includes benefits options. Justworks Hours, Justworks’ time-tracking program, costs an additional per-employee fee per month.
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Our rating: 4.1 out of 5
QuickBooks Payroll is Intuit’s cloud-based payroll product. It goes hand in hand with QuickBooks Online, one of the most popular accounting software solutions around the globe.
If you use both Intuit products, your QuickBooks Online general ledger will update automatically every time you run payroll.
You’ll always have the most up-to-date financial information at your fingertips, which is particularly crucial for nonprofit organizations that are uniquely accountable to donors and other stakeholders.
Honestly, QuickBooks Payroll doesn’t have as many nonprofit-friendly features as most other payroll providers we reviewed here.
However, it does sync perfectly with QuickBooks Online — which, in my opinion, is one of the best accounting programs for nonprofits, large and small.
If you’re used to QuickBooks Online’s outstanding interface and worry about the learning curve you might get with another nonprofit software provider, QuickBooks Payroll is a natural next step.
Our QuickBooks Payroll review can tell you more.
QuickBooks Online Payroll lists pricing for its three payroll plans upfront and online:
While Payroll Core has a higher base price than comparable payroll programs, its higher-tier plans have a lower per-employee fee than most other nonprofit payroll providers. Put another way, the more employees you have, the more money you’ll save with QuickBooks Payroll compared to other providers.
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To learn more about QuickBooks’ accounting module, read our QuickBooks Online review.
We follow a strict set of criteria outlined in our payroll methodology to determine which payroll software to review and to calculate our star ratings.
In addition to the criteria listed on our methodology page, we gave special emphasis to the following data points while reviewing the nonprofit payroll software on this list:
We also use an in-house algorithm to calculate our star ratings which breaks down into the following formula:
We emphasized these factors because nonprofit payroll buyers often need more than basic payroll processing. Predictable pricing helps protect tight administrative budgets, accounting integrations support grant and board reporting, and automation reduces manual work for lean teams.
Payroll decisions are becoming more strategic as nonprofits face rising compensation pressure. Nonprofits saw an average salary increase of 4.77% in the 2025 NonProfit Times survey, matching for-profit industries for the first time in years.
As pay becomes more tied to retention, the right payroll for nonprofits software should support accurate pay, clean reporting, and reliable compliance without adding extra work. It also needs to fit your budget and the way your organization manages people, payroll, and finance.
Now that you know your nonprofit payroll service options, it’s time to start narrowing down your list. If you’re trying to choose between payroll software providers, here are the steps:
Also see: The Payroll Mistakes Experts See Most Often (and How to Avoid Them)
QuickBooks Payroll for nonprofits starts at $50 per month plus $6 per contractor or employee paid per month. Nonprofits can take advantage of 50% for the first three months or opt into a 30-day free trial.
Bear in mind that if you forget to cancel your trial, you’ll be charged automatically for the next month when your trial expires. QuickBooks does not offer refunds.
Yes, 501(c)(3) nonprofits must pay payroll taxes. Payroll taxes include your employees’ federal and state income taxes and FICA taxes (Social Security and Medicare taxes). Nonprofit employers also pay the employer’s share of the employees’ FICA taxes.
Gusto for nonprofits starts at $40 per month, plus $6 per contractor or employee paid per month. If your organization only pays contractors, Gusto costs $6 per contractor paid for the first six months. The price then increases to $35 a month plus $6 per contractor per month.
Managing payroll can be time-consuming and complex, especially for organizations with limited resources that rely on volunteers, grants, and donors to stay afloat. Payroll software helps by automating payroll processes, minimizing tax compliance risk, and saving time so you can focus on your mission instead of on finances. Payroll software can also help you avoid common payroll mistakes that can result in unhappy employees, confused donors, and unwanted messages from the IRS.
Robie Ann Ferrer is an HR expert writer, focusing on HR and payroll software content. She has over eight years of content writing experience, handling different topics. Robie also worked as an HR specialist for 10 years where she managed various facets of HR—from payroll and benefits to employee services and HR systems.
