NonprofitsPayroll

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
  1. ★ Best overall

    Gusto

    Easy to run, month-to-month, and syncs with Aplos, QuickBooks and Xero.

    $49/mo + $6/personVisit
  2. Best for churches and ministries

    OnPay

    Clergy housing pay types, multi-state payroll included, phone support for all.

    $49/mo + $6/workerVisit
  3. Best budget option

    Patriot Payroll

    Lowest monthly cost in this guide for full-service payroll with tax filing.

    $37/mo + $5/workerVisit

Quick comparison

Payroll for nonprofits (US list prices, checked November 12, 2026)
SoftwareFull-service priceCost for 10 employeesMulti-stateSupportLink
Gusto$49/mo + $6/person (Simple)$109/moPlus plan ($80 + $12/person)Phone and chat, business hoursVisit ↗
OnPay$49/mo + $6/worker$109/moIncludedPhone, chat, email, 9am to 8pm weekdaysVisit ↗
Patriot Payroll$37/mo + $5/worker$87/mo$12/mo per extra statePhone, chat, emailVisit ↗

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

#1
★ Best overall

Gusto

Best for small nonprofits that want easy payroll connected to their accounting

$49/mo + $6/personVisit Gusto

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. Tell Gusto during setup that you are a 501(c)(3), so your FUTA exemption is reflected from the first payroll.

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. If you pay a minister a housing allowance, ask Gusto how it handles it before you sign up, and compare OnPay, which has dedicated clergy housing pay types.

#2
Best for churches and ministries

OnPay

Best for churches, ministries and multi-state nonprofits

$49/mo + $6/workerVisit OnPay

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 two clergy housing pay types, one for a housing allowance paid with wages and one for housing the church provides, so the value is kept out of the right tax calculations. It also supports Form 943 filings 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.

#3
Best budget option

Patriot Payroll

Best for small single-state nonprofits watching every dollar

$37/mo + $5/workerVisit Patriot Payroll

What we like

  • Lowest full-service price in this guide
  • Unlimited payrolls; the per-worker fee is charged once a month
  • 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
  • Accounting sync is with Patriot Accounting and QuickBooks; check others
Full Service
$37/mo + $5/worker
Extra states
$12/mo each
Worker fee
Charged once a month per worker paid
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. Patriot syncs with 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 (Clergy Housing Fringe and Clergy Housing Imputed) so the allowance is left out of the right tax calculations. If you are considering Gusto or Patriot, ask how they handle clergy housing allowances before you sign up, and confirm the setup with a tax advisor.

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; check before you pair it with Aplos or Xero.

Sources and updates

Prices and plan details in this guide were last checked against the vendors' own pages on . Vendors change prices often, so confirm the final price on the vendor's site before you buy. Spot something out of date? Tell us and we will re-check it. How we work: editorial policy.

Update history

  • Re-checked every price and plan limit against the vendors' own pages; no changes were needed.
  • Re-checked prices and plan details against each vendor's official pages and corrected what had changed.