8 Best Accounting Software for Nonprofits of 2026

Aplos is built around funds rather than classes, so restricted and unrestricted money stays separated from the first transaction. Its fund accounting page says it can manage multiple funds, grants and projects at once and produce a Statement of Activities and Statement of Financial Position. Lite, at a regular $79 per month, already includes balance sheet and income statement by fund, bank reconciliation, custom reports, a board portal and 1099 management for 2 users. Core, at $129, adds basic budgeting, accounts payable and receivable, recurring transactions, period close and user roles. Grant-level budgets and dimensional reporting sit on Advanced, which Aplos prices from $229 per month with 3 users, and allocations and fixed assets move to Custom. Donation tracking and giving statements are included in every package, which helps small teams that also send donor receipts. The main limits are the 2-user cap on the lower tiers and the jump in price once you need budgets by grant.

FastFund Accounting from Araize is a modular nonprofit system, and its Standard plan packs a lot into $50 per month. Araize lists fund accounting with a six-segment account number, budgeting, project tracking, FASB-compliant financial statements, bank integration, expense and revenue allocations and 990 reporting on Standard. Premium, at $110, adds accrual accounting, accounts payable, accounts receivable and direct cost allocations. Payroll starts at $55 per month and allocates salaries and payroll taxes by fund, grant or program, and FastFund Raising adds a donor database from $50 per month. Very small groups can start with FastFund LT, a $300 per year bundle of accounting and fundraising capped at 250 active donors and 250 active accounts. Support, upgrades and onboarding are included, with no setup fees. The tradeoffs are a cash-basis Standard plan and paid add-ons for extra users, payables and receivables.

QuickBooks Online is not a fund accounting system, but many nonprofits use it because their accountant does. Intuit's pricing page lists class and location tracking, up to 40, on Plus, which is how nonprofits usually tag income and expenses to a program or grant. Plus costs $140 per month at the regular price and also adds budgets and project profitability for 5 users. Advanced, at $340, lifts classes and locations to unlimited, supports 25 users and adds custom permissions, workflows and free 1099 e-filing with Bill Pay Elite. Simple Start at $38 and Essentials at $85 work for a group with one checking account and few restrictions, and the free plan covers basic accounting and invoicing. The weak point is restricted net assets: classes show activity by program, but there is no balance sheet per fund listed among the plan features, so year-end reporting takes more work than in Aplos or FastFund.

Financial Edge NXT is Blackbaud's fund accounting product for nonprofits with complex restrictions. Blackbaud says it tracks grants, projects and endowments in detail with flexible subfunds, and that AI-powered compliance tools enforce purpose and restriction, including anomaly detection and spending controls that stop overspending of a fund. The strongest case for it is the link to Raiser's Edge NXT: gift data, fees and deposits from Blackbaud Integrated Payments can be reconciled automatically, which cuts the usual gap between the development and finance teams. Reporting uses templates designed for nonprofits, customizable dashboards and an AI chat for questions, and view-only licenses let program staff check budgets without full access. Supporting documents can be attached to transactions for auditors. Blackbaud does not publish prices and the page asks visitors to request them, so expect a sales process before you see a number. For a small organization with a few grants, the setup is heavier than Aplos or FastFund.

Fund EZ targets nonprofits that have outgrown general business ledgers, and its feature list reads like a controller's checklist. The chart of accounts is built around funds, programs, grants, departments and funders, and the system keeps the fund balancing entries for you. Budgets can be built by any of those dimensions, can cross fiscal years and can be revised while keeping the original, which grant managers need when a funder approves a budget change. Purchase orders create encumbrances that sit next to budget and actual figures, so managers see what is still available before they commit money, and indirect allocations spread administrative costs across programs and grants. Payables include OCR invoice entry, approvals with separation of duties and 1099 tracking with e-filing. Bank activity comes in through Plaid. Fund EZ does not publish prices, and cloud access comes through Fund EZ Hosted, a managed service, rather than a browser-native app.

MIP Accounting, part of Momentive Software, has served nonprofits and government entities for 40 years and is built for organizations with many funding sources. The vendor says it tracks unlimited funds with a multidimensional chart of accounts, and its core modules cover the general ledger, fund accounting, budgeting, grant reporting, accounts payable and accounts receivable. MIP Cloud ships with more than 340 out-of-the-box reports, configurable dashboards and FASB- and GASB-compliant statements, which matters for nonprofits that report to government funders. Payroll and HR management integrate with accounting, and requisition and purchase order workflows support spending controls. The cloud environment lists SOC compliance endorsed by the AICPA, and MIP says moving existing data to the cloud takes just under 4 hours. The drawbacks are the sales process, since there is no public price, and a setup built for trained finance staff rather than volunteers.

Xero is upfront that it tracks restricted funds with tracking categories instead of dedicated fund accounting. You can set up to four categories, two active at a time, tag income and expenses to a program, grant or funder, give each option its own budget and run a Tracking Summary report. That covers a small nonprofit with a few grants. Its biggest advantage for volunteer-run groups is unlimited general users at no extra cost, so a treasurer, board members and an accountant can share one set of books. Early costs $27 per month at the regular price but caps you at 20 invoices and 5 bills, so most active organizations will need Growing at $59, which adds budgeting with suggestions and auto-reconciliation. Xero offers a nonprofit discount if you raise a case in Xero Central during the trial or within 31 days of subscribing. For Form 990, Xero says it helps prepare the numbers but does not file the return.

Zoho Books is a general small business ledger, and it appears here as the lowest-cost option for very small nonprofits. Its free plan stays free as long as yearly revenue does not exceed $50K and includes invoices, expenses, journals, bank reconciliation, 1099 tracking and a P&L, balance sheet and 50+ reports for 1 user plus an accountant. Standard costs $15 per organization per month billed annually, or $20 monthly, and adds bank feeds, 1099 e-filing, custom fields, custom reports and period locking for 3 users. Professional, at $40, adds project profitability, and budgets sit on Premium at $60. The pricing page does not list fund accounting, restricted net asset reporting or a balance sheet by fund, so a nonprofit with restricted grants will need workarounds or a different tool. For a new group with simple, unrestricted donations, the free plan is hard to beat.