Best Payroll Software for Nonprofits (2026)
We compare Gusto, OnPay and Patriot Payroll for nonprofits and churches: real monthly cost, FUTA exemptions, clergy pay and accounting integrations.
Nonprofit payroll looks like any other payroll until it does not. A 501(c)(3) is exempt from federal unemployment tax but still owes state unemployment. A church may pay its pastor a housing allowance that is taxed differently from salary. Grant-funded staff may need their wages split across programs. Get the setup wrong and you pay taxes you do not owe, or miss ones you do.
We compared three full-service payroll providers that publish their prices, on the things a small nonprofit actually needs: correct tax handling, a real monthly cost, and a clean sync to the accounting system.
Our picks at a glance
3 tools compared- ★ Best overall
Gusto
Easy to run, month-to-month, and syncs with Aplos, QuickBooks and Xero.
$49/mo + $6/personVisit - Best for churches and ministries
OnPay
Clergy housing pay types, multi-state payroll included, phone support for all.
$49/mo + $6/workerVisit - Best budget option
Patriot Payroll
Lowest monthly cost for full-service payroll with tax filing.
$37/mo + $5/workerVisit
Quick comparison
| Software | Full-service price | Cost for 10 employees | Multi-state | Support | Link |
|---|---|---|---|---|---|
| Gusto | $49/mo + $6/person (Simple) | $109/mo | Plus plan ($80 + $12/person) | Phone and chat, business hours | Visit ↗ |
| OnPay | $49/mo + $6/worker | $109/mo | Included | Phone, chat, email, 9am to 8pm weekdays | Visit ↗ |
| Patriot Payroll | $37/mo + $5/worker | $87/mo | $12/mo per extra state | Phone, chat, email, 9am to 7pm ET weekdays | Visit ↗ |
How we chose
A nonprofit’s payroll provider needs to:
- File and pay federal, state and local payroll taxes automatically, including year-end W-2s and 1099s.
- Handle nonprofit tax rules, especially the FUTA exemption for 501(c)(3) organizations, and clergy pay for religious organizations.
- Sync with the accounting system so payroll expenses land in the right funds and programs.
- Publish a clear price, with no long-term contract.
We read each provider’s pricing page and nonprofit or church resources. Large providers such as ADP and Paychex quote prices individually, so we left them out of this comparison. Read more about how we review.
The best payroll software for nonprofits
Gusto
Best for small nonprofits that want easy payroll connected to their accounting
What we like
- Integrates with Aplos, QuickBooks, Xero and FreshBooks
- Unlimited payroll runs on every plan; off-cycle payrolls cost nothing extra
- Month-to-month, cancel anytime
- Health insurance administration at no extra cost when Gusto is your broker
Watch out for
- Simple plan covers single-state payroll only
- Multi-state payroll and time tracking need Plus ($80/mo + $12/person)
- Priority support is a paid add-on on Simple and Plus
- Simple
- $49/mo + $6/person
- Plus
- $80/mo + $12/person
- Premium
- $180/mo + $22/person
- Contract
- Month-to-month
Gusto is the easiest payroll to hand to a part-time office manager. Setup is guided, payroll runs are unlimited, and Gusto files federal, state and local payroll tax forms, including W-2s, 1099s, 940s and 941s.
For nonprofits, the standout is the integration list. Gusto connects directly to Aplos, the fund accounting tool we recommend in our nonprofit accounting guide, as well as QuickBooks and Xero. That means payroll expenses post to your books without re-keying. Gusto also lets you set up tax exemptions, such as the FUTA exemption, in the account.
Which plan to pick: Simple at $49 per month plus $6 per person covers most single-state nonprofits. Choose Plus if you have staff in more than one state or need time tracking.
Watch out for: clergy. Gusto supports clergy tax exemptions but recommends working with a tax advisor on housing allowances. Churches should also look at OnPay.
OnPay
Best for churches, ministries and multi-state nonprofits
What we like
- Dedicated clergy housing pay types for correct withholding
- Multi-state payroll included at no extra cost
- Phone, email and live chat support for every client
- Free account setup and migration of prior payroll data
Watch out for
- HR tools and time tracking are paid add-ons
- Live HR support costs $65 a month extra
- Fewer bundled extras than Gusto's higher plans
- Payroll Essentials
- $49/mo + $6/worker
- Time Tracking add-on
- +$15/mo + $4/worker
- HR add-on
- +$15/mo + $2/worker
- Free trial
- First month free
OnPay’s single base plan includes almost everything a nonprofit needs: unlimited pay runs, federal, state and local tax filings, year-end forms, payroll in all 50 states at no extra cost, and an accounting sync with customizable line-item mapping, so wages can post to the right accounts in your chart of accounts.
It is our pick for religious organizations because it handles their edge cases directly. OnPay offers clergy housing pay types, and its guidance for churches covers excluding FUTA, FICA for clergy, and parsonage allowances from the right calculations. It also supports Form 943 for agricultural workers alongside Form 941.
Watch out for: add-ons. Time tracking, HR tools and live HR support each add to the monthly bill. OnPay sells bundles if you need several.
Patriot Payroll
Best for small single-state nonprofits watching every dollar
What we like
- Lowest full-service price in this guide
- Unlimited payrolls; the per-worker fee is charged once a month
- Free direct deposit (for qualifying customers) and employee portal
- Free USA-based support by phone, email and chat
Watch out for
- Each additional state costs $12 a month
- Time tracking and HR are paid add-ons
- Listed accounting integrations are Patriot and QuickBooks only
- Full Service
- $37/mo + $5/worker
- Extra states
- $12/mo each
- Support hours
- 9am to 7pm ET, weekdays
- Accounting sync
- Patriot, QuickBooks
Patriot keeps payroll simple and cheap. Full Service Payroll files and deposits federal, state and local taxes, handles year-end filings at no extra fee, and guarantees its tax filings. You pay a flat monthly fee plus a per-worker fee once a month, no matter how many payrolls you run. In months with no payroll, you only pay the base fee.
For a 10-person nonprofit in one state, that works out to about $87 per month, roughly $22 less than Gusto Simple or OnPay.
Watch out for: multi-state teams, where the $12-per-state fee adds up, and integrations. The accounting integrations Patriot lists are its own accounting software and QuickBooks, so check before you choose it alongside Aplos or Xero.
Which one should you choose?
- You use Aplos, QuickBooks or Xero and want the smoothest setup: Gusto.
- You are a church or ministry, or have staff in several states: OnPay.
- You are a small, single-state nonprofit on a tight budget: Patriot Payroll.
Whichever you pick, tell the provider during setup that you are a 501(c)(3), so the FUTA exemption and your state unemployment arrangement are configured from the first payroll. If you employ clergy, confirm with a tax advisor how their pay should be set up.
Complete your nonprofit stack: accounting, donor CRM and email marketing.
Frequently asked questions
Do nonprofits pay payroll taxes?
Yes, with one major exception. 501(c)(3) organizations are exempt from federal unemployment tax (FUTA), but they still withhold income tax and pay Social Security and Medicare for most employees. They also have state unemployment obligations, either paying state unemployment tax or reimbursing the state for benefits paid to former employees. Your payroll software needs to be set up with these exemptions.
What payroll software handles clergy housing allowances?
OnPay has dedicated clergy housing pay types that calculate withholding correctly. Gusto supports tax exemptions for clergy but recommends working with a tax advisor on how to record housing allowances. Churches with ministers on staff should confirm this before choosing a provider.
How much does nonprofit payroll cost?
For a nonprofit with 10 employees in one state, expect about $87 to $109 per month with the tools in this guide: Patriot Full Service at $37 plus $5 per worker, and Gusto Simple or OnPay at $49 plus $6 per worker.
Does payroll software connect to nonprofit accounting software?
Gusto lists integrations with Aplos, QuickBooks, Xero and FreshBooks. OnPay syncs to leading accounting software with customizable line-item mapping. Patriot integrates with its own accounting software and with QuickBooks Desktop and QuickBooks Online.