TLDR
Grant fund tracking software must do three things: maintain accurate fund balances per grant, track budget vs. actual against the grant budget period, and produce the report formats grantors actually request. Most accounting tools do the first. Few do all three without Excel. RestrictedBooks is built specifically for this use case. Sage Intacct handles it at enterprise cost.
| Software | Per-Grant Budgets | Budget-to-Actual Report | Restriction Enforcement | Grantor Report Formats | Price |
|---|---|---|---|---|---|
| RestrictedBooks | Yes | Native | Yes | Native formats | $20-$99/mo |
| Sage Intacct | Yes | Native + custom | Yes | Fully customizable | $1,000+/mo |
| Aplos Advanced | Basic | Basic | Limited | Excel needed | $179/mo |
| Blackbaud Financial Edge NXT | Yes | Yes | Yes | Yes | $5,000+/yr |
| QuickBooks Online | No | Manual Excel | No | Manual Excel | $35-$235/mo |
RestrictedBooks
Nonprofit fund accounting with per-grant budget tracking, restriction enforcement, and grantor-ready reports.
Pros
- ✓ Each grant is a structured object with its own budget, period, and restrictions
- ✓ Budget-to-actual report per grant in native format
- ✓ Fund balance enforcement — alerts when grant funds go negative
- ✓ Form 990 Schedule D tracks restricted fund balances automatically
- ✓ Flat pricing at $20-$99/month
Cons
- × Recently launched — less established than older tools
- × No automated federal grant billing workflows
Pricing: $20-$99/month
Verdict: Best choice for bookkeepers managing 5-20 active restricted grants who need more than Aplos's basic tracking and less than enterprise pricing.
Sage Intacct
Enterprise fund accounting with automated grant billing, dimensional tracking, and full grantor report customization.
Pros
- ✓ Automated government grant billing and revenue recognition
- ✓ Dimensional reporting: slice by fund, grant, program, department simultaneously
- ✓ Custom grantor report formats configurable without Excel
- ✓ Multi-grant allocation for shared staff and indirect costs
Cons
- × $1,000-$5,000/month
- × Implementation partner required
- × Complex for small teams
Pricing: $1,000-$5,000/month
Verdict: Best-in-class grant tracking. Only practical for organizations with federal grant portfolios and $10M+ budgets.
Aplos (Advanced tier)
Nonprofit accounting with basic grant tracking on the Advanced plan.
Pros
- ✓ Fund-based accounting tracks grant balances natively
- ✓ Grant tracking module available on Advanced ($179/month)
- ✓ Simpler than enterprise tools
Cons
- × Custom grantor report formats require Excel export
- × Complex indirect cost allocations are manual
- × Grant tracking features thin on Core and below
Pricing: $179/month for Advanced with grant tracking
Verdict: Adequate for organizations with straightforward grant structures. Custom reporting and complex allocations push you to Excel.
Blackbaud Financial Edge NXT
Enterprise fund accounting with grant management capabilities for large nonprofits.
Pros
- ✓ Grant project accounting built into enterprise edition
- ✓ Multi-dimensional fund tracking
- ✓ Integration with Blackbaud grants management tools
Cons
- × Enterprise pricing: $5,000-$15,000+/year
- × Implementation partner required
- × Dual interface complexity during incomplete cloud migration
Pricing: Custom — $5,000-$15,000+/year
Verdict: Strong grant tracking for large organizations. Overbuilt and overpriced for most small nonprofits.
QuickBooks Online with manual Class tracking
General-purpose accounting where grant tracking is a manual workaround using Classes.
Pros
- ✓ Familiar to most bookkeepers
- ✓ Low entry cost
Cons
- × No grant object — each grant is a Class, not a structured record
- × No budget-to-actual per grant without manual spreadsheet
- × No restriction enforcement — negative grant balances go undetected
- × No grantor report format without Excel assembly
Pricing: $35-$235/month
Verdict: Not grant tracking software. Works until the grant complexity grows, then fails at the worst time.
What “grant tracking” actually means
Software vendors use “grant tracking” loosely. It can mean anything from basic tagging to sophisticated multi-dimensional project accounting.
For a nonprofit bookkeeper, grant tracking has specific requirements:
A separate balance per grant. Not a category or a filter — an actual balance that shows how much of the grant remains. When a grant runs out, the balance hits zero. If it goes negative, someone overspent and you have a problem.
Budget-to-actual against the grant period. Grants have budget periods that don’t always align with fiscal years. A two-year grant awarded in March needs tracking against a March-to-March period, not a calendar year. Budget-to-actual shows how much you’ve spent versus what you budgeted — at any point in the grant period.
Indirect cost tracking. Most grants allow a portion of indirect (administrative) costs. Tracking those against the approved indirect rate requires that the allocation methodology runs through the accounting system, not a separate spreadsheet.
Report formats grantors actually use. Every funder has a reporting format. Some use your standard budget-to-actual. Some require a specific line item breakdown. Some want cash basis; others want accrual. Tools that can produce these formats natively save hours per reporting cycle.
The spreadsheet backup problem
Many nonprofits run their grant tracking in a spreadsheet alongside their accounting software. The accounting software tracks the general ledger. The spreadsheet tracks the grant — what was budgeted, what was spent, what remains.
This works until it doesn’t. When the spreadsheet and the accounting system diverge — a journal entry was posted in one but not the other — the bookkeeper discovers it at the worst time: at grant close when the final report is due, or at audit when the auditor asks to tie the spreadsheet to the general ledger.
Software that tracks grants as structured accounting objects eliminates the parallel spreadsheet. The grant balance is computed from actual transactions. There’s nothing to reconcile.
Looking for the right nonprofit accounting software?
RestrictedBooks is purpose-built fund accounting at $99–$249/month flat per organization.
See plans & pricingQ&A
What is the best grant tracking software for a nonprofit bookkeeper?
For nonprofit bookkeepers managing 5-20 active restricted grants without enterprise budgets, RestrictedBooks offers the most complete grant tracking at $20-$99/month. Each grant has its own budget, period, and restriction rules. Budget-to-actual and fund balance reports are native. Sage Intacct is more powerful but starts at $1,000/month. Aplos covers basic grant tracking on the Advanced plan ($179/month) but requires Excel for custom grantor reports.
Q&A
How do I track multiple restricted grants in accounting software without losing track of fund balances?
Each restricted grant should be its own fund in your accounting system — not a tag or Class. When expenses are posted, they go against the grant fund, reducing its balance. The fund balance report shows what remains in each grant. A grant that goes negative means you've overspent the restriction — a compliance problem. Accounting tools that enforce mandatory fund assignment (rather than optional tags) prevent negative balances from going unnoticed.
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