Church payroll is complicated. Between clergy housing allowances, dual-status ministers, FICA exemptions, and quarterly tax filings, running payroll for a church isn’t like running payroll for a regular business. Use the wrong software and you risk costly tax mistakes — or worse, IRS penalties.
We compared the best payroll options for churches on clergy-specific features, ease of use, pricing, and integration with church accounting systems.
Quick Comparison
| Software | Best For | Starting Price | Clergy Housing Allowance | Integrated Accounting |
|---|---|---|---|---|
| OnPay | Churches wanting dedicated church payroll | $36/mo + $6/employee | Yes (built-in) | Yes (QuickBooks, Xero, Aplos) |
| Patriot Software | Small churches on a budget | $17/mo + $4/employee | Manual setup | Yes (Patriot Accounting) |
| Gusto | Churches wanting a modern, easy experience | $40/mo + $6/employee | Manual workaround | Yes (QuickBooks, Xero, FreshBooks) |
| QuickBooks Payroll | Churches already using QuickBooks | $45/mo + $5/employee | Manual setup | Yes (QuickBooks native) |
| Aplos Payroll | Churches already using Aplos accounting | Via ADP | Yes | Yes (Aplos native) |
1. OnPay — Best Overall for Church Payroll
OnPay is the only major payroll provider that offers a dedicated church and ministry payroll product. That means clergy housing allowance handling, minister dual-status reporting, and church-specific tax forms are built in — not bolted on as afterthoughts.
Pros:
- Only major payroll provider with a dedicated church product
- Handles clergy housing allowance, dual-status, and FICA exemption automatically
- Files all federal and state tax forms for you
- Includes workers’ comp and benefits administration
- Integrates with QuickBooks, Xero, and Aplos
- Excellent, US-based customer support
- Free tax penalty protection
Cons:
- Slightly higher base price than some competitors
- Not as many integrations as Gusto
- HR features less robust than dedicated HR platforms
- Benefits admin requires minimum group size
Pricing: $36/month base + $6/month per employee
Best for: Any church that wants payroll done right for clergy without having to manually configure special tax treatment.
2. Patriot Software — Best for Tight Budgets
Patriot is one of the most affordable full-service payroll options available. It handles the basics well and offers integrated accounting, making it a solid pick for small churches that need to watch every dollar.
Pros:
- Lowest starting price of any full-service payroll
- Simple, straightforward interface
- Integrated accounting available (Patriot Accounting)
- Free direct deposit
- Good customer support for the price
- Free tax filing in all 50 states (with Full Service plan)
Cons:
- Clergy housing allowance requires manual setup — not built for it
- No dedicated church/ministry product
- Fewer integrations than competitors
- Limited HR and benefits features
- Reporting is basic
Pricing: Basic $17/mo + $4/employee; Full Service $37/mo + $4/employee
Best for: Small churches with 1-3 staff members who want affordable payroll and are willing to manually configure clergy housing allowance.
3. Gusto — Best User Experience
Gusto is the most user-friendly payroll platform on the market, period. If your church administrator is not a payroll expert and wants software that just works without a learning curve, Gusto delivers. Just know that church-specific tax handling requires manual workarounds.
Pros:
- Best-in-class interface — nearly zero learning curve
- Auto-enrollment tax filings in all 50 states
- Built-in time tracking, PTO management, and employee self-service
- Strong benefits administration (health, 401k, 529)
- Excellent onboarding for new hires
- Integrates with QuickBooks, Xero, FreshBooks, and more
Cons:
- No church-specific product or clergy housing allowance automation
- Minister dual-status requires manual configuration
- Higher cost per employee than Patriot
- Customer support can be slow during peak seasons
- HR features cost extra on higher tiers
Pricing: Simple $40/mo + $6/employee; Plus $60/mo + $9/employee; Premium $80/mo + $12/employee
Best for: Churches with non-payroll-expert administrators who value ease-of-use and are willing to manually handle clergy tax situations.
4. QuickBooks Payroll — Best for QuickBooks Users
If your church already runs on QuickBooks, adding QuickBooks Payroll keeps everything in one system. No syncing, no imports, no separate logins. But like Gusto, church-specific tax situations require manual setup.
Pros:
- Seamless integration with QuickBooks Online — no syncing needed
- Same-day direct deposit available
- Auto tax filing and payments
- Employee self-service portal
- Health benefits and 401(k) available
- Familiar interface for existing QuickBooks users
Cons:
- No church-specific features or clergy housing allowance automation
- Must manually configure minister dual-status and FICA exemption
- Pricing has increased significantly in recent years
- Customer support quality inconsistent
- Limited time tracking in lower tiers
Pricing: Core $45/mo + $5/employee; Premium $75/mo + $8/employee; Elite $125/mo + $10/employee
Best for: Churches already using QuickBooks for accounting who want payroll in the same system and are comfortable manually handling clergy tax situations.
5. Aplos Payroll (via ADP) — Best for Aplos Accounting Users
If your church uses Aplos for accounting and donation tracking, Aplos Payroll (powered by ADP) keeps your financial data centralized. ADP handles the heavy lifting on tax compliance, and the integration with Aplos accounting is seamless.
Pros:
- Seamless integration with Aplos accounting and donations
- ADP handles tax filings and compliance
- Supports clergy housing allowance
- Employee self-service through ADP
- Scalable for growing churches
Cons:
- Requires Aplos accounting subscription (additional cost)
- ADP’s interface is less intuitive than Gusto or OnPay
- Pricing requires a quote — not transparent
- Minimum employee counts may apply
- Less personalized support than dedicated church payroll providers
Pricing: Bundled with Aplos accounting; ADP pricing varies
Best for: Churches already using Aplos who want to keep payroll and accounting in one ecosystem.
How to Choose
1. Do you have clergy on staff?
Yes → OnPay is the only one that handles this automatically. Everything else requires manual setup.
2. What’s your budget?
Under $40/month → Patriot. $40-80/month → OnPay or Gusto. Already paying for QuickBooks? → QuickBooks Payroll.
3. How many employees?
1-5 → Any option works. 6-20 → OnPay or Gusto. 20+ → OnPay or consider ADP directly.
Our Top Pick
For churches with clergy, OnPay is the clear winner. It’s the only payroll provider that actually understands church payroll. For churches without clergy or with just one or two part-time staff, Patriot offers the best value.
SoftDecide helps churches, nonprofits, and small organizations find the right software. Our comparisons are independently researched. We may earn a commission if you purchase through links on this page — at no extra cost to you.