Church payroll services
Published prices start at $17 a month plus $4 per worker for software, $16.50 per payroll run, or $73 a month for a church specialist.
Tell us about your church's payroll
| Service | Price | Clergy pay |
|---|---|---|
| Gusto | $49 a month plus $6 per person | Yes: minister housing allowance earning and FICA exemption setting |
| OnPay | $49 a month plus $6 per worker | Yes: clergy can be marked exempt from FICA |
| Patriot Software Payroll | $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 |
| QuickBooks Payroll (Workforce Payroll) | $50 a month plus $7 per employee (50% off the base for 3 months) | Yes: clergy tax exemption and housing allowance item |
| Paychex Flex | Quote only | Yes: clergy pay and housing allowance (Wespath program) |
| Brotherhood Works payroll (formerly MinistryWorks) | Quote only (call or submit a request form) | Yes: dual tax status and housing allowance |
| ChurchPayroll (Clergytech) | From $16.50 per payroll run | Yes: dual tax status and housing allowance |
| Clergy Financial Resources Church Payroll | From $73 a month (1-2 employees, monthly payroll) | Yes: clergy tax rules, including housing allowance |
Prices from each company's own pricing page. "Quote only" means the company asks you to request a price.
Tell us about your church's payroll
A firm that knows clergy rules replies by email with how it would run your church's pay and what it costs.
Church payroll services run from roughly $17 a month plus $4 per worker for do-it-yourself software up to $73 a month or higher for a firm that manages church pay on your behalf. Price isn't the tricky part. A pastor gets taxed differently from the rest of the staff, and most standard payroll tools don't spell that out. Fill in the short form and you'll receive a written answer about your church.
Why is a pastor's pay different?
For income tax, the IRS counts a pastor as an employee, but for Social Security and Medicare it counts them as self-employed. People often call this split dual tax status. Because of that, the church takes no income tax, Social Security or Medicare out of what a minister earns.
Instead, the pastor covers Social Security and Medicare on their own through SECA, the self-employment tax. With $45,000 in salary plus housing, that's roughly $6,358 for 2026, which works out to about $1,590 each quarter. Our SECA tax calculator lets you check other figures.
The church and the pastor can agree to withhold tax voluntarily so income tax and SECA get covered during the year. That amount lands in box 2 of the W-2, and it keeps the pastor from facing one big tax bill.
The housing allowance on the W-2
The housing allowance is the slice of a pastor's pay the church designates for a home. The tax-free portion is whichever of three figures is smallest: the amount the church designated, what the pastor really spent, or the fair rental value plus utilities. Say the church designated $20,000, actual spending came to $18,500, and rental value plus utilities totaled $24,000. Then $18,500 stays tax-free and $1,500 is taxable. The housing allowance calculator handles other examples.
That tax-free allowance never appears in box 1 of Form W-2. The church can note it in box 14 or on a separate statement. A mistake here throws off the pastor's whole tax return, which is why a firm that handles this every year can be worth having.
Paying other church staff
Workers such as secretaries, musicians and other non-minister staff get taxed like ordinary employees. Their wages are subject to Social Security and Medicare: the church and the worker each pay 6.2% and 1.45%, and the church still has to withhold their income tax. Churches are exempt from federal unemployment tax, and, under an IRS rule for churches and other charities, anyone paid less than $100 in a year has no Social Security or Medicare due on those wages.
Form 941 reports the taxes withheld from staff pay each quarter, with deadlines at the end of April, July, October and January. W-2s for 2026 wages must reach staff, and go to the Social Security Administration, no later than February 1, 2027. A church payroll firm prepares the pastor's W-2, applies the housing allowance and files Form 941 every quarter.
Choosing the right church payroll
Who you pay shapes the right pick. When a pastor is on the payroll, choose a provider that plainly handles the housing allowance and leaves Social Security and Medicare off the pastor's pay. Software costs less, though you're still the one who has to configure those rules correctly.
If you'd rather hand that off, a firm familiar with clergy rules can manage it for you. Complete the short form with your church's name, your email and the number of people you pay. In reply, a payroll or bookkeeping firm emails you with how it would run your church's pay and what that would cost.