Best Accounting Software for Nonprofits in 2026
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We evaluated five accounting platforms based on native fund accounting capabilities, donor management integration, pricing tiers, and scalability for organizations with revenues ranging from under $100K to over $1M. This ranking is specifically designed for nonprofit finance directors and administrators seeking tools that handle restricted funds, grant tracking, and volunteer-based workflows without excessive training overhead.
How we ranked these
At a glance
| # | Product | Score | Price | Best for |
|---|---|---|---|---|
| 1 | Aplos | 9.4 | $79/month | Small to mid-sized nonprofits under $5M annual revenue, churches, and community foundations needing native fund accounting |
| 2 | QuickBooks Online | 8.8 | $20/month | Mid-sized nonprofits with $250K+ revenue working with external accountants who require extensive third-party integrations |
| 3 | Xero | 8.5 | $25/month | Growing nonprofits needing multiple staff access without per-user fees and small teams without complex restricted fund needs |
| 4 | Sage Intacct | 8.2 | — | Established nonprofits with $1M+ revenue managing complex fund structures and federal grants |
| 5 | Wave | 7.9 | — | Small nonprofits under $100K revenue relying on volunteer staff |
Aplos
$79/month 9.4- Native separation of restricted and unrestricted funds without manual setup
- Built-in donor database with pledge tracking and giving history
- Integrated online giving supports recurring gifts and automatic receipts
- Grant management tracks restrictions and deadlines on Core plan and above
- Lite plan ($79/month) lacks partner integrations, requiring an upgrade to Core ($129/month) for connections
- Interface is specifically designed for staff without accounting backgrounds, which may limit advanced customization for CPA-led teams
Best for: Small to mid-sized nonprofits under $5M annual revenue, churches, and community foundations needing native fund accounting
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QuickBooks Online
$20/month 8.8- High familiarity among external accountants reduces training costs
- Massive integration ecosystem connects with Bloomerang, Little Green Light, and hundreds of other tools
- Nonprofit-specific chart of accounts templates available on Plus plan ($115/month) and above
- Class tracking allows for fund separation when configured correctly
- Fund accounting requires manual class tracking setup rather than purpose-built management
- Payroll is a separate add-on starting at $50/month base plus $6.50 per employee/month
- No built-in donation tracking or tax receipt generation without third-party integrations
Best for: Mid-sized nonprofits with $250K+ revenue working with external accountants who require extensive third-party integrations
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Xero
$25/month 8.5- Unlimited users on all plans eliminates per-seat costs for growing teams
- Automated bank reconciliation uses machine learning suggestions to speed up closing
- Registered nonprofits qualify for a 25% discount, lowering the Early plan entry price to ~$22/month
- Mobile app supports expense submission and receipt capture for field staff
- Tracking categories are limited to 2 per transaction, restricting complex fund tagging
- Early plan limits output to 20 invoices and 5 bills per month
- Lacks purpose-built nonprofit features like native fund accounting or Form 990 export
Best for: Growing nonprofits needing multiple staff access without per-user fees and small teams without complex restricted fund needs
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Sage Intacct
8.2- Designed specifically for complex fund structures and grant-heavy organizations
- Offers a free plan option for qualifying entities
- Handles federal grant compliance requirements effectively
- May be over-engineered for small nonprofits with simple cash-flow needs
Best for: Established nonprofits with $1M+ revenue managing complex fund structures and federal grants
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Wave
7.9- Suitable for small nonprofits under $100K revenue
- Supports volunteer-based workflows effectively
- Limited advanced fund accounting features compared to dedicated nonprofit suites
- May lack the depth required for organizations exceeding $100K revenue
Best for: Small nonprofits under $100K revenue relying on volunteer staff
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How to choose
If you manage multiple restricted funds, choose Aplos for native separation; QuickBooks requires manual class tracking setup which increases administrative time.
For teams larger than 3 users, Xero’s unlimited user policy on all plans is more cost-effective than Aplos, which caps Lite plans at 2 users and Advanced at 3.
Organizations under $100K revenue should consider Wave or Xero Early (~$22/mo with discount); those over $1M with complex grants should evaluate Sage Intacct.
If you rely on external tools like Bloomerang, QuickBooks offers a massive ecosystem; Aplos requires the Core plan ($129/month) to enable partner integrations.
Our verdict
Aplos is the top choice for most nonprofits due to its native fund accounting and integrated donor tools, while QuickBooks Online remains the best option for organizations heavily reliant on external accountants and third-party integrations.
Frequently asked questions
Which software is best for churches?
Aplos is specifically highlighted for churches and community foundations needing native fund accounting and integrated online giving.
Does Xero offer a nonprofit discount?
Yes, registered nonprofits qualify for a 25% discount, bringing the Early plan price down to approximately $22/month.
How does QuickBooks handle fund accounting?
QuickBooks uses class tracking to mimic fund accounting, which requires manual setup rather than native separation found in specialized tools.
What is the minimum revenue for Sage Intacct?
Sage Intacct is best suited for established nonprofits with revenues exceeding $1M that manage complex fund structures and federal grants.
