Nonprofit accounting isn’t just small business accounting with a different label. Fund accounting, restricted vs. unrestricted revenue, grant tracking, FASB 116/117 compliance, and Form 990 preparation make nonprofit finances fundamentally different. Using standard business accounting software means workarounds — and workarounds cause errors.
We compared the best accounting platforms built for (or well-suited to) nonprofits on fund accounting capability, reporting, pricing, and ease of use for non-accountant staff.
Quick Comparison
| Software | Best For | Starting Price | True Fund Accounting | Grant Tracking | Form 990 Support |
|---|---|---|---|---|---|
| Aplos | Small nonprofits and churches | $59/mo | Yes | Yes | Partial |
| QuickBooks Online | Nonprofits wanting familiarity | $30/mo | Partial (classes) | Manual | No |
| Xero | Nonprofits wanting double-entry + integrations | $15/mo | Partial (tracking) | Manual | No |
| Sage Intacct | Mid-size nonprofits with complex needs | Custom | Yes | Yes | Yes |
| Wave | Smallest nonprofits on zero budget | Free | No | No | No |
| FUND EZ | Nonprofits wanting dedicated fund accounting | Custom | Yes | Yes | Yes |
1. Aplos — Best for Small Nonprofits and Churches
Aplos is the most accessible true fund accounting software available. If your nonprofit manages multiple funds (restricted, unrestricted, endowment) and you’re tired of QuickBooks workarounds, Aplos handles it natively — at a price small organizations can afford.
Pros:
- True fund accounting built in — no workarounds
- Tracks restricted and unrestricted funds separately
- Built-in donation tracking and donor management
- Automatic contribution statements
- Simple enough for non-accountant administrators
- Built-in reporting for board meetings and grant applications
- Handles fund balances properly (unlike QuickBooks classes)
Cons:
- More expensive than general-purpose accounting tools
- Fewer integrations than QuickBooks or Xero
- Payroll requires ADP add-on
- Advanced reporting is limited compared to Sage Intacct
- Not ideal for nonprofits with complex grant structures
Pricing: Accounting + Donations $59/mo; Accounting only $45/mo; Payroll add-on varies
Best for: Small to mid-size nonprofits (under $2M budget) and churches that need proper fund accounting without enterprise pricing.
2. QuickBooks Online — Best for Familiarity
Many nonprofits use QuickBooks because their bookkeeper or board treasurer already knows it. Class tracking can approximate fund accounting, and the reporting is strong. But “approximate” is the key word — true fund accounting this is not.
Pros:
- Most bookkeepers and CPAs already know it
- Strong reporting and bank reconciliation
- Excellent integration ecosystem
- Good budget tracking by class/location
- Reliable, well-supported platform
- Easy to find QuickBooks-experienced help
Cons:
- Class tracking approximates fund accounting but isn’t the same thing
- No built-in donation tracking
- No grant management
- Fund balance reporting requires manual workarounds
- Doesn’t generate Form 990
- Can misstate net assets if not configured carefully
- Higher-tier pricing adds up fast
Pricing: Simple Start $30/mo; Essentials $60/mo; Plus $90/mo
Best for: Nonprofits with QuickBooks-experienced bookkeepers that don’t manage complex restricted funds and can work with class-based approximations.
3. Xero — Best for Double-Entry + Integration
Xero is a proper double-entry accounting system with a cleaner interface than QuickBooks and better bank reconciliation. Its tracking categories can approximate fund accounting, and its integration ecosystem (1,000+ apps) is the broadest available.
Pros:
- True double-entry accounting — proper financials
- Beautiful bank reconciliation (the best in the category)
- 1,000+ integrations via app marketplace
- Tracking categories approximate fund accounting
- Multi-currency support for international nonprofits
- Clean, modern interface
- Strong project tracking
- More affordable than QuickBooks at similar tiers
Cons:
- Tracking categories are not true fund accounting
- No built-in donation or grant tracking
- No Form 990 generation
- Requires add-on apps for nonprofit-specific features
- Learning curve for non-accountants
- US payroll requires Gusto or ADP integration
Pricing: Starter $15/mo; Standard $30/mo; Premium $55/mo
Best for: Nonprofits that want proper double-entry accounting, strong integrations, and can use tracking categories + add-on apps for nonprofit-specific needs.
4. Sage Intacct — Best for Mid-Size Nonprofits
Sage Intacct is enterprise-grade fund accounting designed for organizations with $2M+ budgets, complex grant structures, and multi-entity reporting needs. It’s what you graduate to when QuickBooks or Aplos can’t handle your complexity anymore.
Pros:
- True fund accounting with full dimensional reporting
- Multi-entity and multi-currency support
- Advanced grant and program tracking
- Automated allocations and revenue recognition
- Form 990 and FASB compliance reporting
- Strong audit trail and controls
- Scales to any size organization
Cons:
- Requires a consultant for implementation ($10K+)
- Monthly cost is significant
- Steep learning curve
- Overkill for small organizations
- Support often requires additional fees
- Long contract commitments typical
Pricing: Custom (typically $400-1,000+/month for mid-size nonprofit)
Best for: Mid-size nonprofits ($2M+ budget) with complex fund structures, multiple grants, or multi-entity reporting needs.
5. Wave — Best Free Option for Tiny Nonprofits
Wave is genuinely free accounting software. For a brand-new nonprofit with a few transactions per month and no restricted funds, Wave covers the basics. But it lacks any nonprofit-specific features, so you’ll outgrow it quickly if your organization gains complexity.
Pros:
- Completely free — no subscription or transaction limits
- Professional invoicing
- Receipt scanning
- Bank and credit card connections
- Basic reporting
- Good enough for simple bookkeeping
Cons:
- No fund accounting whatsoever
- No donation or grant tracking
- No Form 990 support
- Very limited reporting
- Email-only customer support
- No nonprofit-specific features at all
- You’ll outgrow it fast
Pricing: Free (payment processing fees apply if you use Wave Payments)
Best for: Brand-new nonprofits with simple finances, no restricted funds, and zero budget for accounting software.
How to Choose
1. Do you manage restricted funds?
Yes → Aplos or Sage Intacct (depending on budget/size). No → QuickBooks or Xero work fine.
2. What’s your annual budget?
Under $500K → Aplos or Wave. $500K-$2M → Aplos. $2M+ → Sage Intacct.
3. Does your CPA/bookkeeper have a preference?
Yes → listen to them. They’re the ones using it. No → Aplos for fund accounting, QuickBooks for simplicity.
4. Do you need Form 990 preparation?
Yes → Sage Intacct or use a separate 990 tool with any accounting platform. No → any option works.
Our Top Pick
For most small to mid-size nonprofits, Aplos is the right answer — it handles fund accounting properly, tracks donations, and doesn’t require an accounting degree. If you’re very small with simple finances, Wave is free and capable. If you’re larger and complex, Sage Intacct is the professional-grade solution.
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.
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