The one question first: do you need fund accounting?
Fund accounting tracks money by restriction - which grant, which program, which donor-designated purpose - and produces the fund-level statements auditors and grantmakers expect. General small-business accounting does not do this natively; it approximates it with categories or "classes," which means manual workarounds for a true fund-level balance sheet. If you manage restricted grants or endowments, you need real fund accounting. If your money is mostly unrestricted, you can get away with a workaround.
Wave - free, but not fund accounting
Wave's free Starter plan gives unlimited invoicing and bookkeeping at $0/mo, with a $19/mo Pro tier adding automatic bank import and reminders. It is not nonprofit-specific and has no fund accounting at all, so it is unsuitable for restricted funds, grants, or FASB nonprofit statements. Best as a stopgap for very small, all-volunteer, or pre-revenue nonprofits with minimal complexity - plan to migrate once grants appear.
Aplos - native fund accounting
Aplos is cloud fund-accounting built for nonprofits and churches, so fund tracking is the architecture, not a bolt-on. Plans run Lite $79/mo, Core $129/mo (adds budgeting and AP/AR), and Advanced from $229/mo (dimensional reporting by fund, department, and project). Every tier produces true fund-level statements. The trade-offs: prices have risen in recent years, and online giving carries separate transaction fees on top of the subscription. Best for small-to-midsize nonprofits and churches that need real fund accounting without enterprise cost.
QuickBooks via TechSoup - cheapest access, approximate funds
QuickBooks Online is general small-business accounting that nonprofits use with Class and Location tracking to approximate fund reporting - it is not native fund accounting, so restricted-fund balance sheets need manual setup. The reason it is here is cost: through TechSoup, eligible 501(c)(3)s under a $10M budget get a donated annual subscription for an admin fee of about $80/year for the 5-user Plus plan (versus roughly $1,380 direct) or $170/year for the 25-user Advanced plan. Note the "one donated subscription per organization lifetime" rule, and that Intuit has an announced price change effective August 2026. Best for nonprofits comfortable with generic accounting and a broad app ecosystem, without strict fund-level statements.
Blackbaud Financial Edge NXT - the enterprise choice
Financial Edge NXT is enterprise cloud fund accounting with subfund and hierarchical general ledger for restricted funds, endowments, and grants, integrated with Blackbaud's fundraising suite. Pricing is quote-only - Blackbaud publishes no figures, and it is not available through TechSoup. Expect a five-figure annual cost and a real implementation project. Best for larger, complex nonprofits (typically $5M+ budgets) with many restricted funds and existing or planned Blackbaud infrastructure.
How to choose
- Tiny, mostly unrestricted money: Wave (free), planning to migrate as you grow.
- You need real fund accounting on a nonprofit budget: Aplos.
- You can tolerate a workaround and want the lowest cost: QuickBooks via TechSoup (~$80-170/year).
- Large org, complex restricted funds: Blackbaud Financial Edge NXT.
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