If your church is shopping for accounting software, you’ve probably narrowed it down to two names: Aplos and QuickBooks. They’re the most recommended options in church circles, but they solve fundamentally different problems. Pick the wrong one and you’ll be fighting your software instead of using it.
Here’s the straight comparison.
The Short Version
- Choose Aplos if you need true fund accounting, donation tracking, and donor management in one system — and you’re willing to pay more for it.
- Choose QuickBooks if your bookkeeper already knows it, you don’t manage multiple restricted funds, and you want the most widely supported accounting tool on the market.
Where They Agree
Both Aplos and QuickBooks Online:
- Are cloud-based (access anywhere)
- Handle bank reconciliation
- Generate financial reports
- Support multiple users
- Have mobile apps
- Offer free trials
That’s where the similarities end.
Fund Accounting: Aplos Wins (By a Lot)
This is the biggest difference and the one that matters most for churches.
Aplos was built for fund accounting. Restricted funds, unrestricted funds, designated funds, endowments — they’re all tracked separately and correctly. Your building fund balance never accidentally mixes with your general fund. This is how church accounting should work.
QuickBooks uses “classes” and “tags” to approximate fund accounting. It works… sort of. You can track revenue and expenses by fund, but net asset balances don’t track correctly without workarounds. At year-end, you’ll need journal entries to fix fund balances. Your CPA can make it work, but it’s not how QuickBooks was designed to be used.
Verdict: If you manage multiple restricted funds (and most churches should), Aplos handles this correctly by default. QuickBooks requires manual workarounds.
Donation Tracking: Aplos Wins
Aplos has built-in donation tracking. You can:
- Record donations by donor and fund
- Generate year-end contribution statements automatically
- Track giving patterns and donor engagement
- Manage pledges and recurring gifts
- Send giving receipts via email
QuickBooks has no donation tracking. Zero. You’d need a separate tool (like Planning Center Giving, Tithe.ly, or a ChMS) to track donations, then sync the data to QuickBooks.
Verdict: If you want accounting and giving in one system, Aplos. If you’re already using a giving platform, QuickBooks works fine.
Ease of Use: QuickBooks Wins
QuickBooks is the most widely used small business accounting software in the world. Your bookkeeper, treasurer, or CPA probably already knows it. That’s not a small thing — it means zero training time and easy help when you’re stuck.
Aplos is designed for non-accountants, which is great, but it has a smaller user base and fewer resources. When something goes wrong, fewer people can help you troubleshoot.
Verdict: QuickBooks wins on familiarity and available support. Aplos is easier to learn from scratch but has a smaller community.
Pricing: QuickBooks Wins on Base Cost, Aplos Wins on Total Cost
| Feature | Aplos | QuickBooks Online |
|---|---|---|
| Starting price | $59/mo (accounting + donations) | $30/mo (Simple Start) |
| Donation tracking | Included | Not available (need separate tool) |
| Fund accounting | Included | Partial (classes/tags) |
| Payroll | Via ADP add-on | Via QuickBooks Payroll ($45+/mo) |
| Support | Email, chat, phone | Chat, phone (higher tiers) |
QuickBooks is cheaper on paper. But if you add a giving platform ($0-300/mo) and the time cost of workarounds, Aplos is often the same or less total.
Verdict: QuickBooks is cheaper if you already have a giving platform. Aplos is better value if you need both accounting and donations.
Integrations: QuickBooks Wins (By a Lot)
QuickBooks integrates with 750+ apps. Church management tools, payroll, giving platforms, CRMs — if it exists, it probably connects to QuickBooks.
Aplos integrates with a smaller set: QuickBooks (for export), some giving platforms, Stripe, and ADP for payroll.
Verdict: If integrations matter, QuickBooks has a massive advantage.
Reporting: Tie (Different Strengths)
Aplos produces church-specific reports: fund balance reports, contribution statements, giving analytics, and board-ready financials that actually make sense to church leaders.
QuickBooks produces standard business reports: P&L, balance sheet, cash flow. These are accurate but require explanation for church audiences. “Net income” doesn’t mean the same thing in a church context.
Verdict: Aplos reports are ready for church leadership. QuickBooks reports are ready for your CPA.
The Decision Matrix
| Your Situation | Choose |
|---|---|
| You manage multiple restricted funds | Aplos |
| Your bookkeeper knows QuickBooks and doesn’t want to learn something new | QuickBooks |
| You want accounting + donations in one system | Aplos |
| You already use a giving platform (Tithe.ly, Planning Center, etc.) | QuickBooks |
| Your CPA will do the books | QuickBooks |
| A church administrator will do the books (not a CPA) | Aplos |
| Budget under $40/month | QuickBooks (but you’ll need a giving tool too) |
| You need proper fund balance reporting for your board | Aplos |
Our Recommendation
For most small to mid-size churches, Aplos is the better choice. The fund accounting alone is worth the premium. When a church tells us “QuickBooks works fine,” it usually means they’re either not tracking funds correctly or their bookkeeper is doing manual workarounds they shouldn’t have to.
But QuickBooks is the right call if:
- Your bookkeeper or CPA insists on it
- You don’t manage multiple restricted funds
- You’re already using a separate giving platform you’re happy with
- Budget is the primary constraint
Both are good tools. The question is which problem you’re solving: general accounting (QuickBooks) or church-specific accounting (Aplos).
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.