Church payroll and accounting software: costs and minister tax rules
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Payroll for a church with five staff costs $62 to $90 a month at providers that publish prices, from Patriot Full Service ($37 + $5 per worker) to Justworks ($50 + $8), and QuickBooks Workforce bundles payroll with accounting for $120.50, according to their pricing pages (checked October 16, 2026).
The software has to handle ministers correctly: they are employees for income tax but self-employed for Social Security and Medicare, and a housing allowance is excluded from income tax only.
Church payroll is payroll for a congregation's staff, including ministers who are taxed as employees for income tax and as self-employed for Social Security and Medicare, with housing allowances and no FUTA.
Our picks at a glance ranked by published score out of 100
- 1Patriot SoftwareLowest published payroll price$87 a month69See pricing
- 2GustoBest if you want benefits later$109 a month69See pricing
- 3OnPayStaff in more than one state$109 a month67See pricing
- 4Square PayrollSimple payroll for a small staff$95 a month55See pricing
- 5QuickBooks PayrollPayroll and books in one bill$153 a month52See pricing
- 6JustworksPayroll now, PEO benefits later$130 a month42See pricing
On this page
- Quick answer: church payroll and accounting
- What church payroll and accounting cost
- Church payroll and accounting providers
- What makes church payroll different from standard payroll
- Church accounting software: what to look for
- State rules: unemployment, workers' comp and local tax
- Common church payroll mistakes
Quick answer: church payroll and accounting
- Payroll for 5 church staff
- $62 to $90 a monthPatriot to Justworks, published prices
- Payroll plus accounting, 5 staff
- $120.50 a monthQuickBooks Workforce + Simple Start
- Minister Social Security and Medicare
- Paid by the ministerNot withheld by the church
- FUTA for churches
- Not owedSaves $42 per employee a year
Church payroll differs from business payroll in one big way: a minister is an employee for income tax but self-employed for Social Security and Medicare on ministry pay. The church does not withhold or match FICA for the minister, income tax withholding is voluntary, and a housing allowance can be excluded from income tax but not from self-employment tax. Your payroll software needs a pay setup that handles all of that.
We checked these minister rules against IRS Publication 517 (2025), Tax Topic 417 (earnings for clergy), the IRS ministers' compensation and housing allowance FAQ and the Form 4361 and Form 8274 pages, through IRS search results on October 17, 2026. This page gives no dollar limits; work out your own figures from Publication 517 or with your accountant.
What church payroll and accounting cost
| Provider | Published price | 3 staff | 5 staff | 10 staff | What it covers |
|---|---|---|---|---|---|
| Patriot Full Service | $37 + $5 per worker | $52 | $62 | $87 | Payroll only |
| Square Payroll | $35 + $6 per person | $53 | $65 | $95 | Payroll only |
| Gusto Simple | $49 + $6 per person | $67 | $79 | $109 | Payroll only, single-state |
| OnPay | $49 + $6 per worker | $67 | $79 | $109 | Payroll only |
| Justworks Payroll | $50 + $8 per employee | $74 | $90 | $130 | Payroll only |
| QuickBooks Workforce Payroll + Simple Start | $88 + $6.50 per employee | $107.50 | $120.50 | $153 | Payroll plus accounting |
| QuickBooks Workforce Payroll + Essentials | $125 + $6.50 per employee | $144.50 | $157.50 | $190 | Payroll plus accounting |
| Aplos | Not verified for this update | Check | Check | Check | Church and nonprofit accounting |
Source: provider pricing pages, checked October 16, 2026. Count a minister as one person; most providers charge the same per-person fee. Aplos pricing could not be read on October 17, 2026.
A church that already keeps its books in QuickBooks Online can add payroll for the per-employee fee. A church that wants fund accounting and donor tracking built for congregations usually looks at church-specific software such as Aplos and pairs it with a payroll service. Compare the total of both bills, not just payroll.
The table leaves out taxes. For a church, the employer tax bill is often smaller than a business's: no FUTA, no employer FICA on the minister, and in some states no unemployment tax. For non-minister staff, use the employee cost calculator and 2026 SUTA rates.
Church payroll and accounting providers
Payroll services ranked by our published scores. Scores come from our scoring method. Payroll services are scored out of 100 on price transparency and cost for 10 employees (25 points), tax filing coverage and guarantee (20), features (20), contract and exit terms (15), support access (10) and documented complaints (10). Aplos is accounting software and is not scored.
| Provider | Score (out of 100) | Scored as | Watch out for |
|---|---|---|---|
| Patriot Software | 69 | Payroll | Guarantee terms are not published, and each extra state adds $12 a month. |
| Gusto | 69 | Payroll | Tax filing errors are the most common complaint, and the penalty guarantee does not name interest. |
| OnPay | 67 | Payroll | You must give 30 days' written notice to cancel, and slow W-2 corrections are a recurring complaint. |
| Square Payroll | 55 | Payroll | Exit terms and support hours are not published, and mailed paper W-2s cost $3 per form. |
| QuickBooks Payroll | 52 | Payroll | The tax penalty guarantee covers only the top Elite plan, and each extra state costs $12 a month. |
| Justworks | 42 | Payroll | No published tax guarantee or exit terms, and the most common complaint is support that does not resolve issues. |
| Aplos | Not scored | n/a | Church and nonprofit fund accounting |
Source: HRPricing scores dated October 17, 2026, built from published terms and complaints checked October 16, 2026.
Patriot Software
Full Service $37 + $5 per worker: $62 for five staff. Records stay downloadable after you cancel.
How the score adds up
- Price25/25
- Tax filing10/20
- Features8/20
- Contract and exit15/15
- Support5/10
- Complaints record6/10
Gusto
Simple $49 + $6 per person. Full month billed if you cancel after the 5th.
How the score adds up
- Price23/25
- Tax filing14/20
- Features10/20
- Contract and exit12/15
- Support9/10
- Complaints record1/10
OnPay
$49 + $6 per worker with multi-state included.
How the score adds up
- Price23/25
- Tax filing15/20
- Features12/20
- Contract and exit7/15
- Support5/10
- Complaints record5/10
Square Payroll
$35 + $6 per person paid; federal and state filings included.
How the score adds up
- Price24/25
- Tax filing10/20
- Features12/20
- Contract and exit4/15
- Support2/10
- Complaints record3/10
QuickBooks Payroll
Workforce Payroll + Simple Start $88 + $6.50 per employee, or + Essentials $125 + $6.50. Penalty protection only on Workforce Elite.
How the score adds up
- Price15/25
- Tax filing8/20
- Features10/20
- Contract and exit11/15
- Support4/10
- Complaints record4/10
Justworks
Payroll $50 + $8 per employee; PEO plans from $79 per employee.
How the score adds up
- Price21/25
- Tax filing3/20
- Features8/20
- Contract and exit5/15
- Support5/10
- Complaints record0/10
Aplos
Accounting software built for churches and nonprofits. Prices not verified for this update.
What makes church payroll different from standard payroll
| Item | Minister (ministry pay) | Non-minister church staff |
|---|---|---|
| Federal income tax | Taxable; withholding only if the minister asks (voluntary agreement) | Withheld as usual |
| Social Security and Medicare | Not withheld or matched by the church; minister pays self-employment tax | Withheld and matched (7.65% each), unless the church elected out of FICA |
| Housing allowance | Excludable from income tax within IRS limits if designated in advance; still counted for self-employment tax | Not available |
| FUTA | Not owed | Not owed by a church |
| Form W-2 | Yes; wages exclude the housing allowance from income tax boxes | Yes |
Sources: IRS Publication 517 (2025), Topic 417, the Form 4361 and Form 8274 pages and the Section 501(c)(3) FUTA exemption page, checked October 17, 2026 (search results); FICA rate: IRS Topic 751.
- Dual status. Because the minister pays self-employment tax, many ministers make quarterly estimated payments or ask the church to withhold extra income tax to cover it.
- Housing allowance. The board designates it in advance, usually in minutes or a budget resolution. The excludable amount is capped by IRS limits tied to what the minister actually spends on housing and its fair rental value.
- Exemption from self-employment tax. A minister opposed on religious grounds to public insurance can apply for exemption on IRS Form 4361, with a deadline tied to their first ministry earnings.
- Church election out of FICA. A church opposed on religious grounds can elect, on IRS Form 8274, not to pay employer FICA for non-minister staff; those employees then pay self-employment tax themselves.
When you test payroll software, set up a minister with no FICA, voluntary income tax withholding and a housing allowance, then check the W-2 preview. If the software cannot do that, the minister's pay has to be handled outside it.
Church accounting software: what to look for
- Fund accounting. Restricted gifts (building fund, missions) must be tracked separately from the general fund.
- Donor records and giving statements. Year-end giving statements for donors are a church's version of W-2s.
- Payroll link. Either payroll built in, or a payroll service whose journal entries map to your funds and accounts.
- Exit terms. Patriot lets you download W-2s and 941s after you cancel; QuickBooks keeps payroll data for one year after cancellation; Gusto keeps read-only access for admins.
Aplos is accounting software for churches and nonprofits; its prices were not verified for this update.
Larger nonprofits and ministries with staff in several states can compare more providers in payroll for nonprofits and the overall payroll ranking.
State rules: unemployment, workers' comp and local tax
State rules for churches vary. West Virginia lists churches among the exemptions from mandatory workers' comp coverage (W. Va. Code 23-2-1). Many states also exclude church employees from state unemployment coverage, but check your own state agency before you stop filing.
Maryland, a common search for church payroll, taxes church staff wages like any employer's for income tax: state brackets of 2.00% to 6.50% plus county local income tax of 2.25% to 3.30%, withheld by the employer. Maryland's new employer unemployment rate is 2.60% on an $8,500 wage base for 2026. See Maryland payroll taxes and Maryland county income tax rates.
Common church payroll mistakes
- Withholding FICA from a minister's pay. Ministers pay self-employment tax instead.
- Designating the housing allowance after the fact. It has to be designated in advance.
- Treating all staff like the pastor. Secretaries, musicians and custodians are regular employees for FICA unless the church has made the Form 8274 election.
- Paying FUTA. Churches do not owe it; switch it off in payroll.
- Paying a guest speaker with no paperwork. Collect a W-9; 2026 payments of $2,000 or more need a 1099-NEC. See how to pay contractors.
Frequently asked questions
What makes church payroll different from standard payroll?
Does a church withhold taxes from the pastor's paycheck?
What is the cheapest church payroll service?
What is the best church accounting software with payroll?
Do churches pay unemployment tax?
What is a minister's housing allowance?
Sources (22)
- IRS: Topic no. 751, Social Security and Medicare withholding rates (updated Sep 24, 2026; checked Oct 16, 2026)
- IRS: Topic no. 759, Form 940 and FUTA tax (updated Sep 24, 2026; checked Oct 16, 2026)
- IRS: Publication 15 (Circular E), Employer's Tax Guide, for use in 2026 (checked Oct 16, 2026)
- Patriot Software: Patriot payroll pricing (checked Oct 16, 2026)
- Patriot Software: Cancel Patriot software (help article) (checked Oct 16, 2026)
- Square: Square Payroll pricing (checked Oct 16, 2026)
- Gusto: Gusto pricing page (checked Oct 16, 2026)
- Gusto: Cancel your company's Gusto account (checked Oct 16, 2026)
- OnPay: OnPay pricing (checked Oct 16, 2026)
- Justworks: Justworks pricing (checked Oct 16, 2026)
- Intuit: QuickBooks Payroll (Workforce) pricing (checked Oct 16, 2026)
- Intuit: Cancel your QuickBooks Payroll subscription (checked Oct 16, 2026)
- IRS: Instructions for Forms 1099-MISC and 1099-NEC (Dec 2026 revision) (checked Oct 16, 2026)
- West Virginia Legislature: W. Va. Code 23-2-1 (checked Oct 16, 2026)
- Comptroller of Maryland: 2026 Maryland state and local withholding information (checked Oct 16, 2026)
- Maryland Department of Labor: UI trust fund and new employer rate (checked Oct 16, 2026)
- IRS: Publication 517 (2025), Social Security and Other Information for Members of the Clergy and Religious Workers (checked October 17, 2026 (search result))
- IRS: Topic no. 417, Earnings for clergy (checked October 17, 2026 (search result))
- IRS: Ministers' compensation and housing allowance (FAQ) (checked October 17, 2026 (search result))
- IRS: About Form 4361, Application for Exemption From Self-Employment Tax for Use by Ministers (checked October 17, 2026 (search result))
- IRS: Elective FICA exemption: churches and church-controlled organizations (Form 8274) (checked October 17, 2026 (search result))
- IRS: Section 501(c)(3) organizations: FUTA exemption (checked October 17, 2026 (search result))
This page is general information, not tax, legal or accounting advice. Rules and rates change, so check the official source linked above before you file or sign a contract. Read our disclaimer.