Small churches have unique accounting needs that most business accounting software doesn’t handle well. Fund accounting, designated funds, contribution tracking, clergy housing allowances — these aren’t business features, they’re church features. And using business software for church finances means manual workarounds that create errors.

We compared the best accounting options specifically for small churches (under 200 in average attendance) on the features that matter most: fund accounting, ease of use for volunteer bookkeepers, and price.

Quick Comparison

1. ChurchTrac — Best Value for Small Churches

For churches under 200 in attendance, ChurchTrac offers the most features for the lowest price. It includes church management, fund accounting, contribution tracking, and attendance — all in one system. And if your church is under 75 members, it’s completely free.

Pros:

• Free for churches under 75 members (no time limit)
• True fund accounting built for churches
• Built-in contribution tracking and statements
• Attendance tracking included
• Membership management in the same system
• One price covers everything (no modules to add)
• Check-in functionality included
• Background check integration available

Cons:

• Interface is dated — looks like software from 2010
• No native mobile app (mobile-friendly website only)
• Reporting is less customizable than Aplos or QuickBooks
• No built-in payroll (add third-party integration)
• Fewer integrations than larger platforms
• Smaller community = fewer tutorials and resources

Pricing: Free (under 75 members); $29/month (76-150 members); $49/month (151-300 members); $79/month (300+)

Best for: Small churches that want accounting, giving, and membership in one affordable system without paying for features they don’t need.

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2. Aplos — Best for Proper Fund Accounting

Aplos handles fund accounting correctly by default — no workarounds, no classes to configure, no journal entries to fix at year-end. If your church manages multiple funds (building fund, mission fund, youth fund), Aplos tracks each one properly and shows accurate balances for each.

Pros:

• True fund accounting — not a workaround
• Built-in donation tracking and automatic contribution statements
• Clean, modern interface designed for non-accountants
• Handles designated and restricted funds properly
• Fund balance reporting that makes sense to church boards
• Integrates with QuickBooks for export
• Built-in communication tools for donors

Cons:

• More expensive than ChurchTrac or QuickBooks
• Payroll requires ADP integration (additional cost)
• Fewer third-party integrations than QuickBooks
• No membership management (just accounting + donations)
• Reporting could be more customizable for advanced users
• No free plan (14-day trial only)

Pricing: Accounting only $45/month; Accounting + Donations $59/month; Payroll add-on varies

Best for: Churches that need proper fund accounting and donation tracking and want it done right — not approximated with workarounds.

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3. QuickBooks Online — Best if Your Bookkeeper Knows It

Many small churches use QuickBooks because their treasurer or volunteer bookkeeper already knows it. That’s a valid reason — familiarity reduces errors and training time. But you need to understand what you’re giving up (fund accounting) and what you’re gaining (the most supported accounting platform on the planet).

Pros:

• Most bookkeepers and CPAs already know it
• Massive integration ecosystem (750+ apps)
• Excellent reporting and bank reconciliation
• Class tracking can approximate fund accounting
• Strong mobile app
• Built-in payroll option (QuickBooks Payroll)
• Easy to find QuickBooks-experienced help

Cons:

• No true fund accounting — classes/tags are a workaround
• Fund balance reporting requires manual adjustments at year-end
• No built-in contribution tracking (need separate giving platform)
• Doesn’t handle clergy housing allowance calculations
• Monthly costs add up, especially with add-ons
• A volunteer bookkeeper without QuickBooks experience will need training

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

Best for: Small churches whose bookkeeper or CPA already knows QuickBooks and doesn’t need built-in contribution tracking.

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4. FreshBooks — Simplest for Volunteer Bookkeepers

If your church’s bookkeeping is done by a volunteer with no accounting background, FreshBooks is the easiest entry point. It’s designed for people who find accounting intimidating. The interface is clean, simple, and friendly. But it lacks fund accounting entirely, so it’s only suitable for churches with very simple finances.

Pros:

• Easiest accounting interface on the market — period
• Designed for people who are afraid of accounting
• Good invoicing and expense tracking
• Strong mobile app
• Accepts credit cards and ACH
• Good customer support
• Affordable starting price

Cons:

• No fund accounting at all
• No contribution tracking
• Not designed for church-specific tax situations
• Limited reporting for multi-fund organizations
• No payroll
• Only suitable for churches with one general fund and simple finances

Pricing: Lite $19/mo (up to 5 clients); Plus $33/mo; Premium $55/mo

Best for: House churches or very small congregations with one general fund and a volunteer bookkeeper who needs the simplest possible tool.

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5. PowerChurch Plus — Best Desktop Option

Some churches prefer — or require — desktop software. PowerChurch Plus has been serving churches for over 30 years with a one-time purchase model. It includes membership, contributions, accounting, and payroll in a single Windows application.

Pros:

• One-time purchase — no monthly subscription forever
• True fund accounting for churches
• Includes membership, contributions, and payroll
• Data stays on your computer (no cloud concerns)
• Works offline
• Handles clergy housing allowance
• 30+ years of church-specific development

Cons:

• Desktop-only — no remote access or mobile app
• Dated interface (Windows software from the 2000s aesthetic)
• No automatic bank feeds
• Updates and support cost extra
• Windows only (Mac users need virtualization)
• No cloud backup (you handle your own backups)
• Harder to share with remote team members

Pricing: $295 one-time + optional annual support plan ($99-149/yr)

Best for: Churches that want desktop software, a one-time cost, and everything included without monthly subscriptions.

Learn more →

How to Choose: A Quick Decision Guide

How many funds do you manage?

Just one general fund → FreshBooks or QuickBooks. Two or more designated funds → ChurchTrac or Aplos.

Who does the bookkeeping?

A volunteer with no accounting background → FreshBooks or ChurchTrac. A professional bookkeeper → QuickBooks. A church administrator → Aplos.

What’s your budget?

Free → ChurchTrac (under 75 members). Under $30/month → ChurchTrac. $50-60/month → Aplos. One-time purchase → PowerChurch Plus.

Do you need contribution tracking built in?

Yes → ChurchTrac or Aplos. No (you use a separate giving platform) → QuickBooks.

Our Top Pick for Small Churches

ChurchTrac if your church is under 200 members — especially if it’s under 75 (it’s free). You get real fund accounting, contribution tracking, membership management, and attendance in one system for less than most churches pay for just accounting.

Aplos if fund accounting accuracy is your top priority and you want the most polished, church-specific accounting experience available.

QuickBooks only if your bookkeeper insists on it and you’re comfortable with the fund accounting workarounds.

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.