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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.

Get OnPay for Churches →

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.

Try Patriot →

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.

Try Gusto →

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.

Try QuickBooks Payroll →

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.

Learn about Aplos Payroll →

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.

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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.

Running a church involves juggling membership records, event scheduling, volunteer coordination, communication, and giving — often with a small team of staff and volunteers. Church management software (ChMS) brings all of that into one place so you can spend less time on administration and more time on ministry.

We tested and compared the top church management platforms to help you find the right fit for your congregation size, budget, and needs.

Quick Comparison

Software	Best For	Starting Price	Free Plan	All-in-One
Planning Center	Churches wanting modular, pay-as-you-grow tools	Free (basic)	Yes	Partial (add modules)
ChurchTrac	Small churches needing accounting + management	$29/mo	Yes (under 75)	Yes
Breeze	Churches wanting simplicity above all	$69/mo	No (free trial)	Yes
Realm	Mid-size churches wanting deep integration	Custom	No	Yes
Church Community Builder	Large churches with complex needs	Custom	No	Yes
Fellowship One	Very large churches (1,000+ attendance)	Custom	No	Yes

1. Planning Center — Best for Modular Flexibility

Planning Center takes a different approach: instead of one massive platform, you get individual modules (Services, People, Groups, Check-Ins, Registrations, Giving, Resources) that each do one thing really well. Start free, add what you need as you grow.

Pros:

• Generous free tier for small churches
• Only pay for what you use — add modules as needed
• Services module is the gold standard for worship planning
• Excellent check-in system for kids ministry
• Strong mobile apps for each module
• Integrates well with other tools via API

Cons:

• Not truly “all-in-one” — modules feel like separate apps
• Learning curve for administrators
• Giving module is newer and less mature than dedicated giving platforms
• No built-in accounting

Pricing: Free for basic People + Services; paid modules range from $0 (small tiers) to $300+/month for large churches

Best for: Churches that want to start free and grow into paid features only when needed.

Try Planning Center →

2. ChurchTrac — Best Budget All-in-One

ChurchTrac combines church management, accounting, and contribution tracking in one affordable package. It’s the most cost-effective way for a small church to handle everything without juggling multiple subscriptions.

Pros:

• Truly free for churches under 75 members
• Includes accounting, membership, and contributions
• Fund accounting built in
• Simple enough for volunteer administrators
• One price covers everything

Cons:

• Interface feels dated compared to competitors
• Limited customization options
• No native mobile app (mobile-friendly website only)
• Reporting could be more robust
• Smaller user community = fewer tutorials and resources

Pricing: Free (under 75 members), $29-79/month based on size

Best for: Small churches that need the essentials covered in one place without breaking the budget.

Get ChurchTrac →

3. Breeze — Best for Simplicity

Breeze lives up to its name. If you’ve been frustrated by church software that requires a training session just to add a new family, Breeze is the antidote. It’s designed so that anyone on your team — even non-technical volunteers — can figure it out in minutes.

Pros:

• Cleanest, most intuitive interface in the category
• Excellent people management and group communication
• Easy online giving setup
• Good check-in system
• Solid mobile app
• Outstanding customer support

Cons:

• No built-in accounting
• Limited workflow automation
• Reporting is basic
• Higher starting price than some competitors
• Fewer integrations than Planning Center

Pricing: $69/month flat (unlimited people)

Best for: Churches that value ease-of-use above feature depth and want their whole team to actually use the software.

Try Breeze →

4. Realm by ACS Technologies — Best for Mid-Size Churches

Realm is the cloud-based platform from ACS Technologies, a company that’s been serving churches for over 40 years. It’s built for churches that need deep functionality across membership, giving, groups, and — with ACS Financials — accounting too.

Pros:

• Deep feature set across all church management areas
• Strong group and communication tools
• Integrated giving with detailed donor tracking
• Connects to ACS Financials for full accounting
• Mobile app for members and admins
• Backed by a company with decades of church software experience

Cons:

• Pricing requires a demo/call (no published pricing)
• Can feel complex for smaller churches
• Transition from older ACS products can be involved
• Customer support quality varies
• Less intuitive than Breeze or Planning Center

Pricing: Custom pricing based on church size and modules

Best for: Mid-size churches (200-1,000 attendance) that want comprehensive functionality and don’t mind a slightly steeper learning curve.

Learn about Realm →

5. Church Community Builder — Best for Large Churches

Church Community Builder (CCB) has been a go-to for large churches for over a decade. It handles the complexity that comes with multi-staff teams, hundreds of volunteers, dozens of ministries, and high-volume giving.

Pros:

• Built for scale — handles complex org structures well
• Strong process and workflow automation
• Detailed permission system for multi-staff teams
• Robust reporting and analytics
• Good integration ecosystem
• Process templates help standardize ministry operations

Cons:

• Overkill for churches under 300 attendance
• Dated interface compared to newer platforms
• No published pricing — sales process required
• Setup and onboarding can take weeks
• Higher cost than most alternatives

Pricing: Custom pricing, typically $200-500+/month for large churches

Best for: Large churches (500+ attendance) with multiple staff, complex ministry structures, and a dedicated administrator.

Learn about CCB →

How to Choose

Ask yourself these questions:

1. What’s your church size?

Under 100? Planning Center (free) or ChurchTrac (free). 100-500? Breeze or ChurchTrac. 500-1,000? Realm. 1,000+? Church Community Builder or Fellowship One.

2. Do you need accounting built in?

Yes, and budget is tight → ChurchTrac. Yes, and you need robust accounting → Realm (with ACS Financials). No, you use separate accounting software → Planning Center or Breeze.

3. Who’s managing it?

A non-technical volunteer? Breeze. A dedicated admin or IT person? Planning Center or Realm. A pastor wearing all the hats? ChurchTrac.

Our Top Pick

For most churches, Planning Center offers the best balance of free-to-start pricing, flexibility, and quality. If you need accounting included, ChurchTrac is the best value. If simplicity is your top priority, Breeze is worth the premium.

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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.

Choosing the right accounting software for your church isn’t just about tracking dollars — it’s about stewardship, transparency, and keeping your congregation’s trust. Whether you’re a 50-member fellowship or a 2,000-seat sanctuary, the right tool makes fund accounting, payroll, and reporting dramatically easier.

We compared the top church accounting platforms on features, pricing, ease of use, and — most importantly — how well they handle the unique needs of churches (fund-based accounting, designated funds, clergy housing allowance, and more).

Quick Comparison

Software	Best For	Starting Price	Fund Accounting	Free Plan
QuickBooks Online	Small-medium churches wanting familiarity	$30/mo	Partial (tags/classes)	No
Aplos	Churches needing true fund accounting	$59/mo	Yes (built-in)	No (free trial)
ChurchTrac	Small churches on a budget	$29/mo	Yes	Yes (under 75 members)
FreshBooks	Churches with simple bookkeeping	$19/mo	No	No (free trial)
PowerChurch Plus	Churches wanting desktop software	$295 one-time	Yes	No
ShelbyNext Financials	Large churches with complex needs	Custom pricing	Yes	No

1. QuickBooks Online — Best for Familiarity

QuickBooks Online is the most widely used small business accounting software in the world, and many churches use it because their treasurer or bookkeeper already knows it. It’s reliable, well-supported, and integrates with hundreds of other tools.

Pros:

• Most bookkeepers already know it — minimal training
• Excellent reporting and bank reconciliation
• Strong mobile app for on-the-go access
• Class tracking can approximate fund accounting
• Integrates with payroll (via QuickBooks Payroll), bill pay, and more

Cons:

• Not built for fund accounting — you have to use workarounds (classes/tags)
• No built-in contribution tracking or member management
• Doesn’t handle clergy housing allowance calculations natively
• Monthly cost adds up, especially with add-ons

Pricing: Simple Start $30/mo, Essentials $60/mo, Plus $90/mo

Best for: Small to medium churches whose bookkeeper already knows QuickBooks and doesn’t need true fund accounting.

Start free trial →

2. Aplos — Best for True Fund Accounting

Aplos was built specifically for nonprofits and churches. That means fund accounting isn’t a workaround — it’s the foundation. If you manage multiple designated funds (building fund, mission fund, youth fund), Aplos handles this naturally.

Pros:

• True fund accounting built in — not a workaround
• Built-in donation tracking and donor management
• Generates contribution statements automatically
• Handles designated funds, restricted funds, and fund balances properly
• Clean, modern interface designed for non-accountants

Cons:

• More expensive than general-purpose tools
• Fewer third-party integrations than QuickBooks
• Payroll is an add-on (via ADP)
• Reporting can feel limited for advanced users

Pricing: Starts at $59/month for accounting + donation management

Best for: Churches that need proper fund accounting and donation tracking in one system.

Try Aplos free →

3. ChurchTrac — Best for Small Churches on a Budget

ChurchTrac is purpose-built for small to mid-size churches and offers something rare: a genuinely useful free plan for churches under 75 members. It includes accounting, contribution tracking, and membership management in one affordable package.

Pros:

• Free plan for churches under 75 members
• True church-specific fund accounting
• Built-in contribution tracking and member management
• Simple interface that non-accountants can use
• One price includes accounting + membership + contributions

Cons:

• Less polished interface than Aplos or QuickBooks
• Limited reporting customization
• No built-in payroll
• Fewer integrations

Pricing: Free (under 75 members), then $29-$79/month based on membership size

Best for: Small churches that need the basics done right without spending much.

Get ChurchTrac →

4. FreshBooks — Best for Simple Bookkeeping

FreshBooks is designed for freelancers and small businesses, not churches specifically. But if your church has straightforward finances — one general fund, a handful of transactions per month, no complex fund tracking — FreshBooks is the easiest bookkeeping tool on the market.

Pros:

• Easiest interface of any accounting software we’ve tested
• Great for volunteer bookkeepers with no accounting background
• Excellent invoicing and expense tracking
• Strong mobile app
• Good customer support

Cons:

• No fund accounting at all
• No contribution tracking or donor management
• Not designed for church-specific tax situations
• Limited reporting for multi-fund organizations

Pricing: Lite $19/mo, Plus $33/mo, Premium $55/mo

Best for: House churches or very small congregations with simple finances and a volunteer bookkeeper.

Try FreshBooks free →

5. PowerChurch Plus — Best Desktop Option

Most modern accounting software is cloud-based, but some churches prefer — or require — desktop software. PowerChurch Plus is the leading desktop church management and accounting system, and it’s been serving churches for over 30 years.

Pros:

• One-time purchase — no monthly subscription
• True fund accounting built for churches
• Includes membership, contributions, and payroll
• Data stays on your computer (no cloud concerns)
• Works offline

Cons:

• Desktop-only — no mobile access or remote work
• Dated interface
• Updates and support are extra
• No automatic bank feeds
• Windows only (Mac users need virtualization)

Pricing: $295 one-time + optional annual support plan

Best for: Churches that need desktop software, want a one-time cost, or have data security policies that prohibit cloud storage.

Learn more →

How to Choose: 3 Questions to Ask

Still not sure? Answer these three questions:

1. Do you need true fund accounting?

If you manage multiple designated funds (and most churches should), you need software that handles fund accounting natively — not workarounds. That points you toward Aplos or ChurchTrac.

2. What’s your budget?

Under $30/month? ChurchTrac. $50-100/month? Aplos. One-time purchase? PowerChurch Plus.

3. Who’s doing the bookkeeping?

A professional bookkeeper? QuickBooks. A volunteer with no accounting background? ChurchTrac or FreshBooks. A church administrator wearing multiple hats? Aplos.

Our Top Pick

For most small to mid-size churches, Aplos hits the sweet spot. It’s built for churches, handles fund accounting properly, tracks donations, and doesn’t require an accounting degree to use. If budget is tight, ChurchTrac is the best value — especially with its free tier.

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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.