Best Payroll Services for Churches & Ministries (2026)
The best payroll services for churches, ministries and religious organizations are OnPay, Gusto and QuickBooks Payroll, based on support for minister housing allowance and dual tax status of clergy (seca, not fica). Expect $44 to $130 per month for 1 to 10 employees at entry-tier list prices as of November 2026; industry-specific features may require a higher tier.
Prices verified November 2026
What makes payroll harder for churches, ministries and religious organizations
- Minister housing allowance
- Dual tax status of clergy (SECA, not FICA)
- FICA exemption elections
- Small staff, volunteer bookkeepers
What to look for
Clergy payroll is a specialty. OnPay supports housing allowances and clergy tax status natively; Gusto and QuickBooks can be configured but require care.
Our picks for churches, ministries and religious organizations
OnPay
Small businesses, farms, nonprofits and restaurants that want the lowest all-in price with no surprise fees, and free white-glove setup.
Gusto
Teams under 50 who want to run payroll themselves in a few clicks and get benefits, 401(k) and HR tools without a sales call.
QuickBooks Payroll
Businesses already on QuickBooks Online who want payroll to post to the ledger automatically.
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- Prices verified November 2026
Other industries
- Restaurants
- Construction
- Retail
- Medical & Dental Practices
- Nonprofits
- Churches & Ministries
- Salons & Spas
- Trucking & Logistics
- Law Firms
- Startups
- Cleaning & Landscaping
- Franchises
Frequently asked questions
What is the best payroll software for churches, ministries and religious organizations?
OnPay is our first pick for churches, ministries and religious organizations because of clergy payroll is a specialty. Gusto and QuickBooks Payroll are strong alternatives.
How much does payroll cost for churches, ministries and religious organizations?
Entry-tier list prices range from $44 to $130 per month for 1 to 10 employees as of November 2026. Churches & Ministries-specific needs such as minister housing allowance may require an add-on or a higher tier.
Which payroll providers handle minister housing allowance?
OnPay, Gusto, QuickBooks Payroll all support it. Ask any provider to walk you through exactly how before signing.