8 Best Payroll Software for Churches of 2026

OnPay ranks first because its church offer covers the two clergy rules that trip up most treasurers. Its church page says the software automates all tax deductions for non-clergy employees and lets you mark clergy members exempt from Social Security and Medicare, so a pastor and a part-time secretary can sit on the same payroll run with different tax treatment. For housing allowances, OnPay's help center describes a Clergy Housing Fringe pay type for an allowance paid as wages, and a separate imputed setup for church-owned housing, so state withholdings are calculated on each pay run. Pricing is one plan at $49 a month plus $6 per worker, which includes unlimited pay runs and pay schedules, tax filings and payments, and free setup with data migration. A church with one pastor and four staff pays about $79 a month. The limits are that HR features cost extra and the church must still document the allowance amount in advance.

Gusto has the most thorough clergy documentation of any service on this list. Its admin guide for minister and clergy housing allowances explains that Gusto will not calculate federal income tax on a qualified allowance, will not withhold self-employment tax on it because ministers pay that themselves, and totals the allowance in Box 14 of the W-2 at year end. The same guide lists state and local taxes that do apply, including Pennsylvania income tax, Oregon unemployment insurance and paid leave programs in Colorado, Minnesota and Washington. Clergy FICA exemptions are added per employee as special tax exemptions. The Simple plan costs $49 a month plus $6 per person with unlimited payrolls and tax filings, which matches OnPay for a small church. Gusto ranks second because Simple runs payroll in one state only, and time tracking for hourly staff needs Plus at $80 plus $12 per person.

Patriot Payroll is the low-cost choice for churches that are comfortable doing some of the tax work. Its church payroll page lists clergy housing allowance support, and its FAQ tells churches to set up housing allowances as non-taxable money types labeled something like Clergy Housing so they appear in Box 14 of the W-2. A repeating money type saves re-entering the allowance every period, and Auto Payroll runs for staff paid the same each period. Patriot's US pricing page lists Basic Payroll at $17 a month plus $4 per worker and Full Service Payroll at $37 plus $5 per worker, before introductory discounts. Full Service files federal, state and local taxes and Forms 940, 941, W-2 and W-3 at no extra fee, and there are no setup fees. Our checker could not load the pricing page, so the price is marked pending. Basic leaves tax filing to the church, which matters if a volunteer runs payroll.

SurePayroll is the cheapest way on this list to have payroll taxes filed for you. Its Full Service plan costs $29 a month plus $7 per employee and includes unlimited payroll runs, tax filing and deposits, free 2-day direct deposit, and both W-2 and 1099 payments, which suits a church that pays a guest speaker or musician as a contractor. SurePayroll's page for churches and religious organizations names the problems treasurers face, including housing allowances and clergy who are employees for income tax but self-employed for FICA, and says it offers minister payroll tools. Asked directly whether it can handle clergy housing allowances, the page answers yes and says it supports housing allowance setup. A church with one pastor and four staff pays about $64 a month. The trade-offs are a higher per-employee fee than OnPay, 2-day rather than next-day deposit, and less public detail on how clergy settings work.

QuickBooks Payroll is the natural pick for churches that already keep their books in QuickBooks Online. Intuit's help article on clergy payroll shows how to exempt a minister from Social Security, Medicare, FUTA and state unemployment in the employee's tax settings, and offers two dedicated pay types. Clergy Housing (Cash) is for money given to the minister for housing and increases net pay, while Clergy Housing (In-Kind) is for housing the church pays on the minister's behalf and does not. Intuit's US pricing page lists Workforce Payroll at $50 a month plus $7 per employee, with full-service tax filing, auto payroll, unlimited 1099 e-filing and next-day direct deposit. Premium is $88 plus $13 per employee, and Elite at $134 plus $17 adds tax penalty protection up to $25,000 a year. Our checker could not load Intuit's pages, so the price is marked pending. It ranks below Patriot on value because of the higher base fee.

CDM+ Payroll is built for faith-based organizations rather than adapted from small business payroll. The product page lists clergy-friendly settings with separate withholding and reporting exemption options: you can exempt clergy from FICA and Medicare, report Box 1 wages while skipping federal withholding for ministers who pay their own tax, and track clergy amounts in W-2 Box 14. Pay items can run on different schedules, so a semi-monthly salary and a monthly housing allowance can sit on the same employee. Paychecks, employer taxes and deductions post directly to the CDM+ ledger and accounts payable, which keeps fund accounting clean. Tax tables update automatically and quarterly and year-end forms run through Aatrix. CDM+ charges $50 a month for any one program and $25 for each additional program, so payroll plus fund accounting costs about $75. It ranks lower on ease of use because the church still runs and files payroll itself.

Icon Systems sells payroll as an add-on to its church fund accounting, so it suits churches that care most about every payroll entry landing in the right fund. Its church payroll page says pastors' salaries are handled, notes that housing allowances are excluded from income tax but not self-employment tax, and lets the church customize withholdings for pastor salaries on top of automatic withholding. Each employee can use the built-in federal, state and local tax tables or a custom tax formula. The system keeps payroll liability accounts, prints checks to tax agencies and e-files W-2s. Icon Payroll starts at $40 a month and must be added to an accounting package, the cheapest of which is Standard at $35 a month, so expect about $75 a month in total. It scores below CDM+ because the public pages give less detail on clergy settings, and like CDM+ it leaves tax payments to the church.

Paylocity is aimed at larger ministries, multi-site churches and church schools that want payroll, time tracking and HR in one platform. Its page for churches and religious organizations says the software handles housing allowances and ministerial exemptions and lets you account for parsonage allowances for clergy, while its tax services team resolves tax notices on your behalf and gives visibility into federal and state deposits. Custom payroll workflows cover hourly, salary and contract pay. Beyond payroll, staff can clock in by mobile, web, kiosk or timeclock, take assigned training courses, and use a Community hub for chat, file sharing and announcements, which is useful for a school with teachers. The drawbacks for a typical congregation are cost and scale: Paylocity publishes no prices, so you need a quote, and a church with a pastor and three staff will use a fraction of the platform. That is why it scores lowest on value here.