Church payroll software
Published prices and what each service says about clergy pay, side by side.
| Service | Type | Price | Clergy pay | Suits |
|---|---|---|---|---|
| Gusto | Software | $49 a month plus $6 per person | Yes: minister housing allowance earning and FICA exemption setting | Small churches wanting self-serve payroll with HR and benefits add-ons |
| OnPay | Software | $49 a month plus $6 per worker | Yes: clergy can be marked exempt from FICA | Churches wanting low-cost software that handles the clergy FICA exemption |
| Patriot Software Payroll | Software | $17 a month plus $4 per worker paid (Basic Payroll; Full Service Payroll is $37 plus $5 per worker); first 3 months 50% off | Yes: housing allowance setup, W-2 box 14 | Budget-minded small churches that can run payroll themselves |
| QuickBooks Payroll (Workforce Payroll) | Software | $50 a month plus $7 per employee (50% off the base for 3 months) | Yes: clergy tax exemption and housing allowance item | Churches already keeping their books in QuickBooks |
| Paychex Flex | Full-service | Quote only | Yes: clergy pay and housing allowance (Wespath program) | United Methodist churches eligible for the Wespath discount, or churches wanting a large full-service provider |
| Brotherhood Works payroll (formerly MinistryWorks) | Church specialist | Quote only (call or submit a request form) | Yes: dual tax status and housing allowance | Christian ministries wanting a dedicated payroll specialist, especially Brotherhood Mutual insureds |
| ChurchPayroll (Clergytech) | Church specialist | From $16.50 per payroll run | Yes: dual tax status and housing allowance | Churches wanting a clergy-savvy service priced per payroll run |
| Clergy Financial Resources Church Payroll | Church specialist | From $73 a month (1-2 employees, monthly payroll) | Yes: clergy tax rules, including housing allowance | Small churches wanting fixed-rate, all-inclusive payroll with clergy tax help |
Prices as each company publishes them on its own pricing page. "Quote only" means the company asks you to request a price.
Church payroll software does the same job as regular payroll software, with one extra requirement: it needs to get your pastor's pay right. Starting prices tend to run from about $17 a month plus $4 per worker to $73 a month, though a few providers will only share a number once you ask for a quote. What really sets them apart is how each one handles the tax rules that apply to clergy.
A pastor's pay is taxed differently
For income tax purposes, a pastor is usually treated as a church employee, yet counts as self-employed when it comes to Social Security and Medicare. People often call this combination dual tax status. Rather than the church deducting Social Security and Medicare, the pastor covers self-employment tax themselves.
For that reason, a church doesn't take income tax, Social Security or Medicare out of (IRS Publication 15-A) a minister's pay. The two sides can choose to withhold tax voluntarily so that income tax and self-employment tax get covered. Any voluntary federal income tax that is withheld goes in box 2 on the pastor's W-2.
A lot of churches also arrange a housing allowance. This is a slice of the pastor's pay earmarked for housing costs, and it can be free of tax. The church keeps it out of box 1 on the W-2, which is where taxable wages appear. The allowance might instead appear in box 14 or on its own statement.
Good software should let you flag a minister as outside Social Security and Medicare, and it should give you a way to create a housing allowance. If it can't do those two things, you'll end up fighting the software to make it work.
Gusto for churches
Gusto's Simple plan is $49 monthly plus $6 for each person. On its church page, the company says its tools work for clergy and non-clergy employees alike. Its help center walks a church through adding a Minister housing allowance earning and recording a minister's Social Security and Medicare exemption.
Does Paychex work for churches?
With Paychex Flex, pricing comes by quote only, and churches don't come up on its small business page. That said, Wespath, the United Methodist benefits agency, notes on its partner page that Paychex brings experience with clergy payroll and housing allowances. Organizations in the United Methodist fold can also claim a 35% discount through Wespath's program.
QuickBooks Payroll for a church
Workforce Payroll runs $50 a month plus $7 per employee. It's a natural pick when your church's bookkeeping already lives in QuickBooks. Intuit publishes a help article that walks through exempting clergy from payroll taxes and creating a housing allowance item for clergy.
Payroll services built for churches
A handful of providers focus solely or mostly on churches:
- Brotherhood Works, once known as MinistryWorks, says its staff takes care of dual tax status and housing allowances. Pricing comes by quote.
- ChurchPayroll also provides payroll audits, corrections and support when dealing with the IRS.
- Clergy Financial Resources describes itself as specializing purely in church payroll and clergy tax matters.
Questions churches often ask
Can Gusto run clergy payroll?
According to Gusto, clergy employees fall within what its tools cover. Its help center shows how to add a Minister housing allowance earning and record a minister's exemption from Social Security and Medicare withholding.
Is there a QuickBooks for churches?
The published pricing shows no dedicated church edition. Churches simply take the standard Workforce Payroll plan and follow Intuit's help article to configure the clergy exemption and housing allowance.
Should a pastor's W-2 show Social Security wages?
No. The IRS says a minister's Form W-2 and Form 941 should omit Social Security or Medicare wages and withholding. Whichever software you pick should keep those boxes blank for your pastor.
What self-employment tax could a pastor owe?
In 2026, a pastor with $60,000 of salary and housing combined would owe around $8,478, which works out to about $2,119 per quarter. That estimate relies on IRS Publication 517 together with the 2026 Social Security wage base. Voluntary withholding through church payroll is one way some pastors manage the bill.