Running a small nonprofit feels a lot like trying to herd cats while balancing on a budget tightrope. You’ve got restricted grants that can’t mingle with general funds, donors who want to know exactly where their $50 went, and a volunteer treasurer who still thinks QuickBooks is “fancy.” Enter the hero you didn’t know you needed: the best fund accounting software for small nonprofits.
Fund accounting isn’t optional—it’s the DNA of nonprofit financial integrity. Mess it up, and you risk losing grants, donor trust, or (gulp) your tax-exempt status. The great news? In 2025, you no longer need a six-figure budget to get rock-solid fund tracking. Let’s break down the absolute best options tailored for small nonprofits—because your mission deserves precision without the price tag.
Why Small Nonprofits Can’t Afford to Skip True Fund Accounting
Think of your organization’s money like colored water in separate jars. One jar is “Emergency Shelter Grant—only for beds.” Another is “General Donations—use anywhere.” Regular business accounting dumps everything into one giant bucket. Fund accounting keeps those colors pure.
I’ve watched tiny nonprofits get red-flagged in audits because they used Wave or Cash App alone (great tools, wrong job). The best fund accounting software for small nonprofits automatically segregates restricted vs. unrestricted funds, generates perfect Form 990 reports, and makes your board sigh with relief instead of panic.
Top 7 Best Fund Accounting Software for Small Nonprofits (2025 Edition)
1. Aplos – The Gold Standard for Growing Nonprofits
Aplos was literally built by a church planter who got tired of spreadsheet chaos. Today it’s the darling of small-to-mid-sized nonprofits.
- True fund accounting with unlimited funds
- Built-in donor management + online giving
- Automatic allocation rules (e.g., 10% of every donation to admin)
- Gorgeous board reports in two clicks
Pricing: Starts at $79/month but offers a 15% lifelong nonprofit discount. Worth every penny once you cross $100K in revenue.
2. MoneyMinder – Perfect for PTAs, Clubs, and Micro-Nonprofits
If your budget is under $150K and your treasurer is a volunteer parent, MoneyMinder is pure joy.
- Designed by a former PTA treasurer (she gets the struggle)
- Simple fund tracking without the jargon
- Built-in 990-EZ guidance
- Only $179/year (or less for the ultra-basic “Gem” plan)
I’ve personally moved three PTAs to MoneyMinder—they went from crying over Excel to sending perfect reports in under 30 minutes.
3. Nonprofit+ (by Araize FastFund) – Hidden Gem for Serious Fund Tracking
Don’t let the clunky name fool you. Nonprofit+ is a beast disguised as a budget-friendly suite.
- Full fund accounting + payroll + grant tracking
- Unlimited users and transactions
- Starts at just $49/month for the core module
Best part? They’ll import your old data for free if you ask nicely.
4. Xero with Nonprofit Add-ons – The Flexible Powerhouse
Yes, Xero is “for-profit” software—but pair it with apps like Gusto or Fathom and you get surprisingly robust fund tracking.
- Use “Tracking Categories” as pseudo-funds
- Beautiful bank feeds and mobile app
- Free for churches and many 501(c)(3)s through special programs
Pro tip: Combine Xero with the free tier of Fathom for nonprofit-specific dashboards. Many small orgs use this combo as their best fund accounting software for small nonprofits under 250K.
5. QuickBooks Online + Nonprofit Template (with a Twist)
Before you roll your eyes—hearth this out. QuickBooks Online Plus + the free nonprofit chart of accounts template from the Nonprofit Accounting Basics group actually works amazingly well.
- Classes + Locations = makeshift funds
- 50% nonprofit discount brings it down to ~$35/month
- Every CPA already knows it
It’s not perfect, but it’s familiar and scalable.
6. Zoho Books (Free or Low-Cost Tier) – Sneaky Good Option
Wait—didn’t we talk about Zoho in our guide to free accounting software for nonprofits 2025? Yes! And its paid tiers ($20–$50/month) add legit fund accounting through custom fields and projects. Great stepping stone if you’re graduating from truly free tools.
7. GnuCash (100% Free, Open-Source) – For the Brave and Tech-Savvy
If your budget is literally zero and you have a volunteer who speaks “double-entry,” GnuCash handles unlimited funds offline. Steep learning curve, but unbeatable price.
How to Choose the Best Fund Accounting Software for Your Small Nonprofit
Answer these five questions honestly:
- What’s your annual budget? (<$150K → MoneyMinder or free tools; $150K–$750K → Aplos or Nonprofit+)
- How restricted are your funds? (Lots of grants = need true fund accounting, not tracking categories)
- Who’s your treasurer? (Volunteer parent = simple interface; CPA on board = more power OK)
- Do you need built-in donation/CRM tools? (Yes → Aplos; No → Xero or Nonprofit+)
- Are you planning to grow fast? (Choose something scalable so you don’t migrate again in 18 months)
The Biggest Mistake Small Nonprofits Make (and How to Avoid It)
Using general accounting software and “making it work” with classes or tags. It feels fine… until your first big grant audit. Suddenly you’re spending 80 hours untangling which expenses came from which fund. The best fund accounting software for small nonprofits does the heavy lifting automatically.
Final Verdict: My Top 3 Picks by Situation
- Best Overall: Aplos (just trust me—your future self will thank you)
- Best Budget-Friendly: MoneyMinder (under $200/year and zero headaches)
- Best Free-ish Upgrade Path: Start with the free accounting software for nonprofits 2025 options, then graduate to Zoho Books or Xero when you’re ready
Your mission is too important for duct-taped finances. Pick one of these tools today, and turn your treasurer from stressed-out volunteer into confident financial ninja.
Ready to stop guessing and start knowing exactly where every dollar lives? Try Aplos free for 15 days here (no card required), or grab MoneyMinder and sleep better tonight.
