Most accounting software uses "classes" or "tags" to simulate fund accounting. That breaks when you need real restricted fund tracking, proper financial statements, or Form 990 reporting. Alignmint is built from the ground up for nonprofit fund accounting with a pre-built chart of accounts that maps directly to Form 990 line items. For a full evaluation guide, read our nonprofit accounting software comparison.
Fund accounting software for nonprofits should show which money is restricted, which money is available, and how every gift, grant, bill, reimbursement, and deposit affects your reports. Generic bookkeeping tools can record transactions, but nonprofit fund accounting keeps donor purpose, Form 990 reporting, and board-ready statements connected.
Start with clean funds, deposits, bills, and reports before spreadsheet habits turn into year-end cleanup.
Track restricted gifts and grants by purpose so spending, balances, and funder reports stay clear.
Connect donations, accounting, reimbursements, and reports so staff and board members trust the same numbers.
Every feature designed for how nonprofits actually work, not retrofitted from small business software.
Track restricted, temporarily restricted, and unrestricted funds with real-time balances. See exactly how much is available in each fund at any moment with as many funds as you need.
Your accounts are already set up and mapped to Form 990, so you can start tracking right away. Add custom accounts as needed. Every account is categorized for proper nonprofit financial reporting.
Complete transaction history with running balances. Filter by fund, account, date range, or transaction type. Drill down into any entry. Export to CSV or Excel.
Create manual or automatic journal entries with Draft, Posted, and Voided statuses. Full audit trail for every change. Memorized transactions for recurring entries with auto-posting schedules.
Generate Balance Sheet, Cash Flow Statement, Income Statement, Income Statement by Fund, and Comparative Reports. Export to PDF or Excel. All reports meet nonprofit accounting standards.
Auto-generate Form 990 worksheets from your chart of accounts. Pre-mapped line items mean less manual work at year-end. Export worksheets for your CPA or file directly.
Use true fund accounting when classes, tags, and spreadsheets no longer give your board or CPA enough confidence.
Track donor restrictions, program funds, grants, campaigns, and board-designated funds with balances that stay visible all year.
Use a nonprofit chart of accounts mapped to Form 990 lines so year-end reporting does not become a manual translation project.
Donations, pledges, events, grants, volunteer in-kind value, and fiscal sponsor fees flow into accounting without import cleanup.
For buyer research, compare the broader nonprofit accounting software guide, the best nonprofit accounting software guide, our free accounting software for nonprofits guide, and our nonprofit chart of accounts template.
Generic accounting software wasn't designed for nonprofits. Here's what breaks.
| Capability | QuickBooks / Xero | Alignmint |
|---|---|---|
| Fund Tracking | "Classes" or "Tags" (workaround) | Native restricted fund tracking |
| Form 990 | Manual mapping required | Pre-built chart of accounts, already mapped |
| Fund Balances | Not supported natively | As many fund balances as you need |
| Donor Integration | Requires third-party CRM | Built-in donor CRM |
| Nonprofit Accounting Standards | Manual configuration | Built-in, audit-ready statements |
Comparing church platforms? See how Alignmint handles Planning Center accounting gaps and Realm accounting software for churches that need donor records, contribution tracking, and fund accounting in one place.
How does Alignmint compare to other options for nonprofit fund accounting?
| Feature | Alignmint | QuickBooks ("Classes") | Aplos |
|---|---|---|---|
| True Fund Accounting | ✓ | — (class workaround) | ✓ |
| Restricted Fund Tracking | ✓ | — (manual tagging) | ✓ |
| Sub-Funds | ✓ (unlimited) | — | Limited |
| Form 990 Prep | ✓ (pre-mapped) | — (manual mapping) | ✓ |
| Free Tier | ✓ (under $100K) | — | — (trial only) |
| Donor CRM Built-in | ✓ | — | Basic |
Comparison data as of May 2026. Features and pricing may change.
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Free plan available. No credit card required.
