What accounting software is best for a small nonprofit?

For small nonprofits, Alignmint offers the best combination of features and price — it's free for organizations up to $100K in annual donations and includes true fund accounting, donor management, and financial reporting. Aplos is another option if you only need accounting, but it charges $59+/month and doesn't include CRM or volunteer tools.

Can small nonprofits use QuickBooks?

You can, but it's not ideal. QuickBooks doesn't support fund accounting natively — it uses 'classes' which aren't the same as true funds. You can't track restricted vs. unrestricted balances properly, and your financial statements won't meet nonprofit accounting standards without significant manual adjustments.

Is there free accounting software for nonprofits?

Yes. Alignmint's Starter plan is free for nonprofits with up to $100K in annual donations and includes fund accounting, donor CRM, and financial reporting. Wave is free but designed for small businesses, not nonprofits — it lacks fund accounting and donor management entirely.

Do small nonprofits need fund accounting?

Yes. If you receive any restricted gifts, grants, or designated donations, you're required to track them separately from general operating funds. This is a nonprofit accounting standard, not optional. Fund accounting software makes this automatic instead of manual.

Best Accounting Software for Small Nonprofits: 2026 Guide

Running a small nonprofit means doing more with less. Your budget is tight, your team is small, and you still have the same compliance requirements as organizations ten times your size. The wrong accounting software makes everything harder. The right one gives you back hours every week.

This guide compares the best accounting software for small nonprofits in 2026 — with honest assessments of what each option does well and where it falls short.

Why Small Nonprofits Can't Use Generic Accounting Software

It's tempting to use QuickBooks, Wave, or even Excel. They're familiar, they're cheap (or free), and they handle basic bookkeeping. But nonprofits aren't small businesses, and the differences matter:

Fund Accounting vs. Business Accounting

Small businesses track income and expenses. Nonprofits track income and expenses by fund. When a donor gives $1,000 to your youth program, that money is restricted — you can't spend it on rent. When a grant covers staff salaries for a specific project, those expenses must be tracked against that grant.

This is called fund accounting, and it's not optional. It's required by nonprofit accounting standards and expected by auditors, grantors, and your board.

QuickBooks handles this with "classes" — but classes aren't funds. You can't see a true fund balance, you can't track restrictions, and your financial statements won't be formatted correctly for nonprofit reporting. Here's a detailed breakdown of why QuickBooks falls short.

Donor Management

Small businesses don't have donors. Nonprofits do. Your accounting software should know who gave what, when, and for what purpose. It should generate year-end giving statements automatically. It should let you segment donors for targeted communications.

Generic accounting software doesn't do any of this. You'd need a separate CRM — which means two systems, double data entry, and monthly reconciliation.

Compliance Reporting

Nonprofits file Form 990, produce statements of functional expenses, and report to grantors with specific budget formats. Generic accounting software doesn't generate these reports. You'd need to export data and build them manually in spreadsheets.

What to Look For

Here's what matters most when you're evaluating accounting software for a small nonprofit:

1. True Fund Accounting

Not "classes" or "tags" — actual funds with their own balances, restrictions, and reporting. You should be able to see at a glance how much is in your general fund, your building fund, your scholarship fund, and every grant.

2. Affordable (or Free) Pricing

Small nonprofits shouldn't pay $500/month for accounting software. Look for transparent pricing with no per-user fees. A genuine free tier (not a 14-day trial) is ideal — it lets you test the platform with real data before committing.

3. Built-in Donor Management

If your accounting software includes a donor CRM, you eliminate the need for a separate system. Every donation flows to both the donor profile and the general ledger automatically. No double entry.

4. Financial Reporting That Meets Standards

Your software should generate these reports without manual work:

Balance sheet (statement of financial position)
Income statement (statement of activities) — by fund
Statement of functional expenses
Budget vs. actual
Form 990 schedules

5. Ease of Use

Your executive director or bookkeeper will use this software — not a CPA. It needs to be intuitive enough for someone without an accounting degree. If the learning curve is weeks instead of hours, your team won't adopt it.

6. Grant Tracking

Even small nonprofits manage grants. Your software should let you set up grant budgets, track spending against them, and generate funder reports without exporting to spreadsheets.

Want to try fund accounting for free? Schedule Your Free Setup | Explore Features

Comparison: Best Accounting Software for Small Nonprofits in 2026

Pricing as of February 2026. Check vendor websites for current pricing.

Feature	Alignmint	Aplos	QuickBooks Online	Wave	Xero
Fund accounting	Yes (true funds)	Yes	No (classes only)	No	No
Donor CRM	Yes (built-in)	Basic	No	No	No
Online donations	Built-in	Add-on	No	No	No
Volunteer management	Yes	No	No	No	No
Event management	Yes	No	No	No	No
Form 990 reports	Yes	Yes	No	No	No
Financial statements	Nonprofit-formatted	Nonprofit-formatted	Business-formatted	Business-formatted	Business-formatted
Bank connection	Yes	Yes	Yes	Yes	Yes
Free tier	Up to $100K donations	No	No	Yes (limited)	No
Starting price	Free	~$59/mo	~$30/mo	Free	~$15/mo
Per-user fees	None	None	Yes ($10/user)	None	None

Alignmint

Best for: Small nonprofits that want everything in one platform.

Alignmint is the only option on this list that combines fund accounting, donor CRM, volunteer management, event planning, and marketing in a single platform. The Starter plan is genuinely free for nonprofits with up to $100K in annual donations — not a trial, not a stripped-down version.

The main limitation: Alignmint is newer than some competitors, so it may lack some niche features that established platforms have built over decades.

Aplos

Best for: Small nonprofits that only need accounting and basic donor tracking.

Aplos is a solid nonprofit accounting platform with true fund accounting and decent reporting. It's been around for years and has a loyal user base. The downside: it doesn't include volunteer management, event tools, or marketing — and pricing starts at ~$59/month with no free tier.

QuickBooks Online

Best for: Small nonprofits with very simple finances and no restricted funds.

QuickBooks is familiar and affordable, but it's not built for nonprofits. No fund accounting, no donor management, no nonprofit-formatted reports. If you receive any restricted gifts or grants, QuickBooks will create compliance headaches. Read our detailed comparison.

Wave

Best for: Very early-stage nonprofits with zero budget and minimal needs.

Wave is free and handles basic bookkeeping. But it has no fund accounting, no donor management, no nonprofit reporting, and limited support. It's a temporary solution at best.

The Real Cost Comparison

Don't just compare subscription prices. Compare the total cost of getting what you need:

What You Need	Alignmint	Aplos + Mailchimp + Eventbrite	QuickBooks + Bloomerang
Accounting	Included	~$59/mo	~$30/mo
Donor CRM	Included	Not included (need separate)	~$99/mo
Email marketing	Included	~$20/mo	~$20/mo
Event management	Included	~$0 (per-ticket fees)	~$0 (per-ticket fees)
Volunteer tools	Included	Not included	Not included
Monthly total	$0 (Starter)	~$79/mo+	~$149/mo+
Annual total	$0	~$948+	~$1,788+

For small nonprofits on the Starter plan, Alignmint saves $1,000-2,000/year compared to cobbling together separate tools — and you get better integration and less manual work.

How to Get Started

Assess your needs: List what you need today (fund accounting, donor tracking, online giving) and what you'll need in 12 months
Try the free tier: Sign up for Alignmint's Starter plan and import your data — no credit card required
Import your history: Bring over your donor list, donation history, and chart of accounts via CSV
Set up your funds: Create funds for each restricted purpose (grants, designated gifts, programs)
Connect your bank: Link your bank account for automatic transaction import
Generate your first reports: Run a balance sheet and income statement to verify everything imported correctly

Small nonprofits deserve the same quality tools that large organizations use — they just can't afford the same price tag. That's why the best accounting software for small nonprofits isn't a stripped-down version of enterprise software. It's a modern platform built for your reality: limited staff, tight budgets, and no room for workarounds.

Schedule Your Free Setup | Explore Features

Related:

Nonprofit Accounting Software — Complete guide to nonprofit accounting
Better Than QuickBooks for Nonprofits — Why purpose-built wins
Best Free Nonprofit Software in 2026 — Honest comparison of free options
Fund Accounting Software — What fund accounting is and why it matters
Fund Accounting — See how Alignmint handles fund accounting