Best Bookkeeping Software For Nonprofits

Nonprofits face unique accounting challenges that for-profit businesses don’t. You need to track multiple funding sources, each with its own rules, and prove you’re spending every dollar the way donors intended. Using bookkeeping software can simplify grant and donor management, saving you hours of work and letting you focus on your mission.

Software	Price	Verdict
Aplos	$39.50/mo	Best for full-featured fund accounting and donor reporting
ZipBooks	$0/mo	Best free starter for simple invoices and bank sync
MonkeyPod	$199/mo	Best all-in-one CRM, fundraising, and fund accounting
FastFund Online	$50/mo	Best for audit-ready grant tracking and fund reports
QuickBooks Online	$35/mo	Best familiar platform with basic fund tagging
Wave	$0/mo	Best free, easy invoicing and expense tracking

Factors to Consider

Nonprofit organizations need help tracking restricted and unrestricted funds as well as managing grants and donors. The right platform gives you a complete financial picture and keeps your organization in good standing:

• Fund accounting — separate restricted funds (like a donation for a new building) from unrestricted funds, manage grants, and sort costs into program services, management and general, and fundraising to stay audit-ready.
• Donor management and tracking — store donor contact details, automatically issue donation receipts and thank-you letters, and track pledges and recurring donations.
• Budgeting and forecasting by fund or program — build a detailed budget for each fund, program, or grant, and compare actual spending side-by-side with your budget in real time.
• Reporting for stakeholders — clear reports for board members, donors, grantors, and regulators, including grant-level spending reports and Form 990.
• Audit trails — a step-by-step log of every transaction, who entered it, and when it was changed, with locked entries.
• Volunteer management (optional) — record hours, tasks, and skills for in-kind donation data and engagement reports.

1. Aplos

Aplos stands out as a complete nonprofit software solution by combining fund accounting, donor management, and financial reporting in one cloud platform. It offers true fund accounting with balance sheets and income statements by fund, built-in donor tracking, automated receipts, and 1099 management. Plans run Lite ($39.50), Core ($64.50), and Advanced ($229). The downsides are that advanced budgeting and dimensional reporting are top-tier only, and the price point is higher for large nonprofits.

2. ZipBooks

ZipBooks provides a simple, cloud-based solution for nonprofits that need easy accounting. While true fund accounting is not included, its free and low-cost plans cover invoicing, bank reconciliation, and project tracking — ideal for small organizations on a tight budget. Its free Starter plan includes unlimited invoices and vendor tracking, with Smarter ($15) and Sophisticated ($35) tiers above. The main gaps are the lack of true fund accounting and built-in donor management.

3. MonkeyPod

MonkeyPod offers a true nonprofit-in-a-box solution that merges accounting software, donor relations, and grant management. Its fund accounting tools keep restricted and unrestricted funds clear, while donor and fundraising features streamline acknowledgments and online giving (with Stripe integration). It also includes unlimited email sends and campaign automation. Plans run Essentials ($199), Pro ($349), and Enterprise ($499), so it’s a higher monthly price than basic accounting software.

4. FastFund Online

FastFund Online is designed to simplify fund accounting and reporting for charities and nonprofits. It offers true fund accounting with a customizable chart of accounts, automated financial statements including IRS Form 990, and project and expense tracking for grants and events. Plans run Standard ($50) and Premium ($110), with add-on modules for accounts payable/receivable and indirect allocations. There’s no free plan.

5. QuickBooks Online

QuickBooks Online offers a familiar, cloud-based accounting solution that nonprofits can adapt to their needs. While it doesn’t provide true fund accounting out of the box, its class and location tools let you segment income and expenses by program. Auto-imported bank transactions and easy invoicing cut down on manual data entry, and built-in reports give you the visibility you need for board meetings and grant compliance. Plans run Simple Start ($35) to Advanced ($235).

6. Wave

Wave offers nonprofits a no-cost way to handle basic financial management in one place. Its free Starter plan covers the essentials — bank sync, invoicing, and standard reports — so you can keep transactions organized without fees. When you need more automation, the Pro plan ($16) adds auto-categorization and receipt scanning. The main gaps are the lack of true fund accounting and grant tracking, with payroll and receipt scanning as paid add-ons.

Simplify Fund Tracking

Nonprofit organizations need bookkeeping software to bring together fund accounting, grant management, donor tracking, and real-time financial reporting in one place. This way, you can separate restricted and unrestricted dollars, automate donor receipts and grant spend reports, and run audit-ready statements at the click of a button. Feeling swamped by the numbers? Partner with EpicBooks for tailored bookkeeping services to maximize your nonprofit’s finances and fuel your impact.