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.

Factors to Consider When Choosing Nonprofit Accounting Software

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

Fund accounting is an important factor to look for because it helps you keep track of every dollar in the right place. With it, you can separate restricted funds, like a donation for a new building, from unrestricted funds that pay for everyday expenses. You’ll also be able to manage grants by tracking how each grant is spent and meeting any reporting rules set by the funder.

The platform should let you run reports by program or project so you can see exactly how each activity is performing financially. Look for a system that lets you sort costs into different categories, such as program services, management and general, and fundraising. This way, you keep your books audit-ready, making your donors stay confident in your handling of their gifts.

Donor Management and Tracking

It’s also good to have a donor management database right in the software, so you can store each donor’s contact details. With this feature, you’ll always know how much someone has given and whether they prefer email updates or mailed newsletters. 

The software should let you automatically issue donation receipts and send personalized thank-you letters right after a gift is made. It should also track pledges and manage recurring donations, so you can see upcoming gifts, send reminders if a payment is missed, and forecast your income more accurately. 

Budgeting and Forecasting by Fund or Program

With budgeting and forecasting features, you can build a detailed budget for each fund, program, or grant, assigning costs like salaries, supplies, and event expenses to the correct accounts. This level of detail helps you plan exactly how donor funds will be used and shows where money is needed most. The software can then display your actual spending side-by-side with your budget in real time, so you can spot any gaps or overruns right away. 

By monitoring budget vs. actuals for each fund or program, you can make quick adjustments and keep your projects on track.

Reporting for Stakeholders

Your nonprofit needs clear, accurate reports for board members, donors, grantors, and regulators to show how you’re using funds and meeting goals. You can also pull donor-specific reports to show supporters exactly how their gifts were spent, which builds trust and encourages future giving. For grantors, the system can create grant-level spending reports that match funder requirements and deadlines. And when it’s time to file with government agencies, you’ll have the documents you need, like Form 990. 

Audit Trails

Audit trails keep a step-by-step log of every transaction, who entered it, and when it was changed. This record helps you and your auditors trace any donation, expense, or transfer back to its source for full transparency. With it, you can spot mistakes or unusual activity quickly and correct them before they become bigger problems. The software should lock each entry so no one can delete or alter past records without leaving a clear note of what was changed and why. 

Volunteer Management (Optional)

While not every bookkeeping system includes volunteer tracking, having this feature can add real value to your nonprofit. With volunteer management, you can record each person’s hours, tasks, and skills in the same software you use for your finances. That means when a grant asks for in-kind donation data, you can easily show how many hours volunteers contributed and what services they provided. 

You’ll also be able to run reports on volunteer engagement, helping you recognize top contributors and plan future events.

Best Bookkeeping Software for Your Nonprofit Organization

Use nonprofit accounting software to keep funds on track, stay audit-ready, and simplify reporting. Aplos, ZipBooks, Monkeypod, FastFund Online, QuickBooks Online, and Wave offer unique features that offer solutions that best fit your size, budget, and reporting needs.

1. Aplos

Basic Features

• Fund accounting with Balance Sheet and Income Statement by fund
• Bank reconciliation and custom report builder
• Donor management with automated receipts and giving statements
• 1099 management and unlimited customer support
• User roles, permissions, and third-party integrations

Pricing Plans

Overview

Aplos stands out as a complete nonprofit software solution by combining fund accounting, donor management, and financial reporting in one cloud platform. Its clear fund-based reports help your organization show donors and boards exactly how money is used, while automated tools reduce manual work.

2. ZipBooks

Basic Features

• Send and customize unlimited invoices and payment reminders (invoicing)
• Connect bank accounts for real-time transaction imports
• Auto-categorize expenses and flag vendor details
• Run simple income statements and balance sheets
• Access intelligent feedback to improve financial management

Pricing Plans

Overview

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. This is ideal for small organizations on a tight budget. Smart insights and auto-categorization keep your books clean, so you spend less time on data entry and more time serving your community. 

3. Monkeypod

Basic Features

• Fund accounting with chart of accounts and real-time grant budgets
• Automated gift acknowledgments, donation tracking, and donor insights
• End-to-end grant management: proposal tracking, reminders, and expense reports
• Embedded online fundraising pages with Stripe integration for payments
• Unlimited email sends and email campaign automation

Pricing Plans

Overview

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. Plus, with built-in email marketing and advanced reporting, your team can manage finances and supporter engagement from one platform. 

4. FastFund Online

Basic Features

• Fund accounting with budgets and automated year-end closing entries
• General ledger, bank integration, and bank reconciliation
• Automated recurring entries and custom financial statements
• Duplicate detection and audit trails for secure transaction records
• Dedicated support and regular data migrations

Pricing Plans

Overview

FastFund Online has customizable chart of accounts and automated statements, which offers more reliable data for board reports and grant compliance. With optional add-ons for payables, receivables, and allocations, you can tailor the software to match your organization’s size and needs.

5. QuickBooks Online

Basic Features

• Connect multiple bank and credit card accounts for real-time transactions
• Auto-categorize income and expenses with rules and tags
• Create and send branded invoices with online payment links
• Track classes, locations, and accounts to mimic fund accounting
• Generate Profit & Loss, Balance Sheet, and Cash Flow reports
• Invite multiple users with customizable access levels

Pricing Plans

Overview

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 financial visibility you need for board meetings and grant compliance. 

6. Wave

Basic Features

• Send unlimited invoices and estimates, and accept payments online
• Auto-import and categorize bank and credit card transactions
• View built-in Profit & Loss and Balance Sheet reports
• Manage receipts with free mobile capture (receipt add-on for OCR)
• Invite collaborators and set basic user permissions

Pricing Plans

Overview

Wave offers nonprofits a no-cost way to handle basic financial management and bookkeeping software needs in one place. Its free Starter plan covers the essentials, bank sync, invoicing, and standard reports, so you can keep your organization’s transactions organized without worrying about fees. When you need more automation, the Pro plan adds auto-categorization and receipt scanning to cut down on data entry.

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. Get your free quote today to maximize your nonprofit’s finances and fuel your impact.