What is the best payroll software for a nonprofit in 2026?
Good nonprofit payroll gets the 501(c)(3) setup right, costs what you planned, and doesn't need a payroll expert to run.
Your nonprofit just hired its first staff member, or you have eight people and the spreadsheet is starting to break. You need payroll that files taxes for you, handles part-time and contract staff, and doesn't charge you for features you'll never touch.
The short answer. OnPay is our top pick: one plan at $49 a month plus $6 per worker, filings included. QuickBooks Payroll wins if your books already live in QuickBooks. Patriot is the cheapest full-service option at $37 plus $5 per worker. Square Payroll suits contractor-heavy teams at $6 per contractor with no base fee. ADP RUN fits nonprofits growing past 50 staff.
What other roundups skip: a 501(c)(3) is exempt from federal unemployment tax (FUTA), but only if your payroll is set up that way. We compared every tool with that setting, and grant cost tracking, in mind.
The ranking is editorial: a sponsored spot is always labeled on its card, and no affiliate link changes a score.
The best nonprofit payroll for your situation
5 payroll tools for nonprofits
This ranking is for the executive director, treasurer or operations lead of a US nonprofit with 1 to 50 staff. Each tool was compared on how well it fits a 501(c)(3) and on the price its vendor publishes.
| Best for | What sets it apart | Free plan | Team size | Visit | ||||
|---|---|---|---|---|---|---|---|---|
| 1 | OnPay | Best overall for nonprofits | One flat plan with tax filings included | 4.3/5 | $49/mo + $6/worker | — | Nonprofits with 2 to 50 staff | Visit → |
| 2 | QuickBooks Payroll | Best if your books are in QuickBooks | Payroll and accounting in one place | 4.1/5 | From $88/mo + $6.50/employee | — | Nonprofits already on QuickBooks Online | Visit → |
| 3 | Patriot Payroll | Cheapest full-service payroll | Lowest published full-service price | 4.0/5 | $37/mo + $5/worker | — | Nonprofits with 1 to 20 staff, tight budgets | Visit → |
| 4 | Square Payroll | Best for contractor-heavy teams | Contractor-only plan with no base fee | 3.8/5 | $35/mo + $6/person | — | Nonprofits paying mostly contractors or event staff | Visit → |
| 5 | ADP RUN | Best for growing nonprofits | Deep compliance and HR packages | 3.7/5 | Quote only | — | Nonprofits heading past 50 staff | Visit → |
Scores on five weighted criteria, detailed in the method. Prices read in 2026 on each vendor's official pricing page, in US dollars.
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How we compared and scored
A nonprofit doesn't buy payroll like a startup. It has part-time program staff, contractors, grant-funded roles, and often a volunteer treasurer. So we weighted nonprofit fit first, then real cost. A price only counts if it appears on the vendor's own pricing page: ADP publishes none and scores lower on cost for it.
We compared vendor pricing pages, IRS guidance for exempt organizations and public user reviews. We didn't open accounts. Scores match our main payroll software ranking so they stay consistent across pages.
- Nonprofit fitHandles a 501(c)(3) setup cleanly: FUTA exemption, part-time and seasonal staff, contractors, grant-funded roles, multi-state staff.35 %
- Real costPrice published on the vendor's own pricing page for a 5 to 25 person team, base fee plus per-person fee.25 %
- Ease for a small teamCan an executive director or volunteer treasurer run payroll without a payroll background?20 %
- Tax filing and supportFederal and state filings, W-2s and 1099s handled, and real people to call when a filing goes wrong.10 %
- User feedbackPublic reviews, recurring complaints, and comments from small nonprofit employers.10 %
No affiliate link changes a score or a rank.
Payroll prices change every year. Get the updates
OnPay
OnPay keeps it simple: one payroll plan, $49 a month plus $6 per worker. There is no cheap starter tier that hides tax filings behind an upgrade. For a 10-person nonprofit, that is about $109 a month. Federal and state payroll taxes, W-2s and 1099s are part of the plan.
That flat pricing is what makes it our top pick for nonprofits. Small charities often mix part-time program staff, seasonal workers and a few contractors. OnPay pays all of them on the same plan, at the same per-worker fee.
Its limit: OnPay lists nonprofits as an industry it serves, but its pricing page shows no nonprofit discount. And it is a payroll tool first. If you need deep HR, performance reviews or a large benefits catalog, you will outgrow it.
Tip: before you run your first payroll, ask OnPay to confirm your organization is set up as FUTA-exempt. A 501(c)(3) does not owe federal unemployment tax, and a wrong setting means paying a tax you can't waive back easily.
- $49/mo + $6 per worker
- One plan, filings included
- Employees and contractors on one plan
- ✓Predictable price
- ✓Covers employees and contractors
- ✓Easy for a non-specialist
- ✗No nonprofit discount listed
- ✗Light HR features
- ✗HR add-on costs extra
The safest default for a small 501(c)(3). If your books already live in QuickBooks, weigh QuickBooks Payroll before you sign.
QuickBooks Payroll
QuickBooks Payroll makes sense for one reason above all: your accounting is already in QuickBooks. Payroll entries then post straight into your books, which matters when you have to show a funder how much of a salary went to a specific program.
The pricing page lists bundles, not payroll alone. Workforce Payroll with Simple Start costs $88 a month plus $6.50 per employee. With Essentials, $125 plus $6.50. Premium with Plus, $203 plus $10. New plans ran at 50% off for three months in 2026. For 10 staff on the entry bundle, expect about $153 a month at full price.
Its limit: it costs more than OnPay or Patriot for the same payroll. Part of what you pay is accounting you may already have, or not need.
Tip: map each employee to a class or location for each program. Your Form 990 functional expense split gets much easier at year end.
- Payroll posts to QuickBooks
- Class and location tracking
- Bundles with accounting
- ✓No double entry
- ✓Strong tax filing
- ✓Widely known by bookkeepers
- ✗Pricier than standalone tools
- ✗Bundles you may not need
- ✗Accounting bundle required
A strong pick when QuickBooks is already your ledger. If it isn't, OnPay or Patriot does the payroll part for less.
Patriot Payroll
Patriot is the budget pick. Full Service payroll costs $37 a month plus $5 per worker, with federal, state and local filings done for you. For 5 staff, that is about $62 a month. The Basic plan drops to $17 plus $4 per worker, but then you file payroll taxes yourself.
For a nonprofit with one or two staff and a volunteer treasurer, Full Service is the version to buy. The Basic plan saves $20 a month and costs you hours of filing and the risk of late penalties.
Its limit: each additional state adds $12 a month on Full Service. If your staff work remotely across several states, that fee adds up and OnPay becomes cheaper. The interface is plain, and integrations are thinner than QuickBooks.
Tip: Patriot runs a 50% off promotion for the first three months. Start in a quiet month so you learn the tool before a busy grant reporting season.
- $37/mo + $5 per worker
- Tax filings on Full Service
- Basic plan from $17
- ✓Lowest full-service price
- ✓Clear published pricing
- ✓Good fit for 1 to 10 staff
- ✗$12/mo per extra state
- ✗Plain interface
- ✗Fewer integrations
The cheapest safe option for a tiny nonprofit in one state. Multi-state teams should run the numbers against OnPay.
Square Payroll
Square Payroll has the cheapest entry point for one specific case: if you only pay contractors, the contractor-only plan costs $6 per person paid, with no monthly base fee. A nonprofit that runs on freelance instructors and a few event workers pays only for the months it pays them.
With employees, full service costs $35 a month plus $6 per person. That is close to Patriot and below OnPay on the base fee.
Its limit: Square Payroll is built around shift work and Square's point of sale. It has fewer tools for salaried program staff, grant-funded roles or nonprofit reporting. Support also scores below the leaders in public reviews.
Tip: if you only pay contractors, stay on the contractor plan. It has no base fee, so a month with no payments costs nothing.
- $6 per contractor, no base fee
- Full service from $35/mo
- Pay only for months you pay
- ✓Cheapest for contractors
- ✓Simple setup
- ✓Good for event staff
- ✗Thin nonprofit reporting
- ✗Weaker support reviews
- ✗Built for retail shifts
A smart pick if most of your people are contractors. For salaried staff, OnPay or Patriot fits better.
ADP RUN
ADP RUN is the payroll tool of the largest payroll company in the US. It handles payroll, filings, new hire reporting and, in higher packages, HR support and benefits. For a nonprofit growing past 50 staff across several sites, that depth is the reason to call ADP.
ADP sells four packages, Essential, Enhanced, Complete and HR Pro, all on quote. You won't see a number before a sales call.
Its limit: price. Small nonprofits often find ADP too big for what they need, and add-ons stack up.
Tip: ask for the total annual cost in writing, with every add-on and year-end form fee included, then compare it to OnPay at the same headcount.
- Four packages up to HR Pro
- Large compliance team
- Benefits administration
- ✓Scales with large teams
- ✓Strong compliance help
- ✓Wide HR coverage
- ✗No public prices
- ✗Too big for small teams
- ✗Add-ons stack up
Worth a quote once you pass 50 staff. Below that, you pay for depth you won't use.
What nonprofit payroll really costs each month
Base fee plus per-person fee, at the prices vendors publish in 2026. ADP is quote only and left out.
For 5 staff
Patriot Full Service: $62. Square full service: $65. OnPay: $79. QuickBooks with Simple Start: $120.50, accounting included.
For 15 staff
Patriot: $112. Square: $125. OnPay: $139. QuickBooks with Simple Start: $185.50. The gap between Patriot and OnPay stays under $30 a month.
With staff in three states
Patriot adds $12 a month per extra state on Full Service, so $24 more for two extra states. Ask every vendor about per-state fees: for a remote team, the cheapest tool on paper is not always the cheapest bill.
- Is your organization set up as FUTA-exempt?
- Are tax filings included, or do you file yourself?
- Is there a fee per extra state?
- Can you pay contractors and employees on one plan?
- Can you track payroll by program or grant?
- Is the price published, or quote only?
Other options worth knowing
These come up often in searches. They're not ranked because their pricing isn't on their own site, or they serve a different need.
Gusto: popular, but price not readable on its site
Not rankedGusto shows up in nearly every nonprofit payroll roundup. We couldn't read its pricing on its official page this year, and we found no published nonprofit discount. Until we can source its price, it stays out of the ranking.
- Status
- Price not sourced
Paychex Flex: quote only, built for scale
QuotePaychex sells to nonprofits of all sizes, on quote. User reviews often call it too big for a small team. Compare it to ADP once you pass 50 staff.
- Price
- Quote only
Your CPA's payroll service
Hands-offMany small nonprofits let their CPA run payroll. It costs more per run, but it also covers your Form 990 and audit questions. Ask which software the firm uses: often one on this list.
- Best for
- No in-house finance
What breaks nonprofit payroll
These mistakes show up again and again. None of them appear on a pricing page.
Paying FUTA you don't owe
TaxA 501(c)(3) is exempt from FUTA, and the exemption can't be waived. If your payroll tool isn't told, it calculates and files the tax anyway. Check your first payroll report line by line.
- Check
- FUTA set to exempt
Calling staff contractors
ComplianceSmall nonprofits often pay regular program staff as contractors to save time. If the person works set hours under your direction, they are likely an employee, and back taxes follow.
- Risk
- Back taxes and penalties
Forgetting remote staff states
CostEach state where an employee works needs its own registration and filings. Some tools charge per state. Map where your people live before you pick a plan.
- Patriot
- +$12/mo per state
Pay less for payroll without the risk
Simple habits that lower the bill, whatever tool you pick.
Start during a promotion
PricePatriot and QuickBooks both ran 50% off for three months in 2026. Start in a quiet month and you learn the tool while it costs half.
- Saving
- Up to 50% for 3 months
Tag payroll by program from day one
ReportingSet up classes or departments per program before your first run. Your grant reports and Form 990 functional expenses then come straight from payroll data.
- Gain
- Faster year-end reports
Switch on January 1
MigrationA January switch means no year-to-date wages to load and one provider per W-2. If you can't wait, switch at the start of a quarter.
- Gain
- Clean W-2s
Want payroll to sync with your books and donor tools? Get our automation guides
Go further
These pages pick up where this one stops.
Our ranking of nonprofit accounting tools.
You want to compare all payroll toolsBest payroll softwareOur main payroll ranking.
You manage members, donors and volunteersNonprofit management softwareTools to run your organization.
Your questions on nonprofit payroll
Do nonprofits pay FUTA tax?
No, not if you are a 501(c)(3). The IRS says a section 501(c)(3) organization is exempt from FUTA tax, and the exemption can't be waived. Other exempt organizations may owe it. Make sure your payroll tool is set up as FUTA-exempt from day one.
Do nonprofits withhold Social Security and Medicare?
Yes. A 501(c)(3) is subject to Social Security and Medicare taxes like any employer, with narrow exceptions such as some church organizations. Exempt organizations with employees also withhold federal income tax.
What is the cheapest payroll for a small nonprofit?
Patriot Full Service, at $37 a month plus $5 per worker with tax filings. If you only pay contractors, Square's contractor-only plan costs $6 per person with no base fee.
Is there free payroll software for nonprofits?
Not with tax filings included among the tools we compared. Patriot's Basic plan costs $17 a month plus $4 per worker, but you file taxes yourself. For a volunteer-run nonprofit, the filing risk usually outweighs the savings.
Should a nonprofit use a PEO or payroll software?
Payroll software is enough for most small nonprofits. A PEO becomes interesting when you want access to larger group benefits, but it takes more control and costs more per employee.
How do I split payroll costs across grants?
Track each employee's hours by program or grant, then post payroll by class or location in your accounting tool. QuickBooks Payroll does this natively. With other tools, export the payroll journal and allocate it in your books.
Can I switch payroll providers mid-year?
Yes, but the new provider must load your year-to-date wages and taxes so W-2s are correct. Switching at a quarter start keeps your quarterly filings clean, and January 1 is easiest of all.
