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Best Accounting Software for Nonprofits Shortlist

Before getting into the details of nonprofit accounting software, here’s who made the cut:

  1. Aplos - Best for donor management
  2. FreshBooks - Best for basic expense tracking
  3. Zoho Books - Best for nonprofits using other services from Zoho
  4. ZipBooks - Best for unlimited invoicing
  5. Xero - Best for customization
  6. QuickBooks - Best for tracking cash flow by project
  7. Realm - Best for churches
  8. Wave - Best for ease of use
  9. Quicken - Best for individually-run nonprofits
  10. Serenic Navigator - Best for range of features
  11. NetSuite - Best for enterprise and international nonprofits
  12. Sage Intacct - Best for global nonprofits

Accounting software is non-negotiable for organizations that need to track their money and keep their books balanced.

This is especially true for nonprofit organizations–maybe even more so–since they’re not only keeping track of their own money but that of their donors they've been entrusted with as well.

In this article, I’ll break down some of the best nonprofit accounting software to help you find the right one for your organization.

Overview of the 12 Best Accounting Software for Nonprofits

1. Aplos - Best for donor management

Aplos cash dashboard screenshot
Aplos offers a simple dashboard that lets you track your nonprofit’s key performance indicators. (Image Source)

Why I picked Aplos: Aplos is a program that offers easy-to-use accounting tools without sacrificing functionality. It also has a powerful donor-management system to help you stay connected with donors.

Aplos Standout Features and Integrations:

Standout features include CRM tools that let you create donor profiles, track your communication and relationship history with them, make tailored appeals for donations, and track the pledges donors offer. The service also comes with fund accounting, donation tracking, online giving forms, reporting, and budgeting tools.

Integrations include many services, including Gusto, WePay, Church Community Builder, Bloomerang, PayPal, Sage Payroll, and more.

Price: From $79 a month

Free Trial: 15 days

  • Donor management tools
  • Intuitive and easy to use without sacrificing functionality
  • Many integrations
  • High price
  • Some basic services require higher level of subscription

2. FreshBooks - Best for basic expense tracking

FreshBooks revenue dashboard showing charts
FreshBooks works across multiple platforms and has a simple dashboard for tracking your nonprofit’s finances. (Image Source)

Why I picked FreshBooks: FreshBooks is a low-cost option that comes with the tools that small nonprofits need, including expense tracking and the ability to accept payments.

FreshBooks Standout Features and Integrations:

Standout features include tracking restricted funds to ensure you don’t spend your nonprofit’s donations improperly. It also offers services like expense tracking, reporting tools, and time tracking to help manage your nonprofit. You can also use its invoicing tools and payment acceptance service to get paid if you provide work or a service for someone else.

Integrations include Hubspot, Gusto, Fundbox, Zapier, and more.

Price: From $17 a month (or 6 months for $6.80/mo with current promotion)

Free Trial: 30 days

  • Low cost
  • Long trial period
  • Track restricted funds
  • Fewer features aimed specifically at nonprofits
  • $10 monthly fee for each additional user

3. Zoho Books - Best for nonprofits using other services from Zoho

Zoho Books invoice dashboard
Zoho lets you track sales, purchases, inventory, and more from a single dashboard. (Image Source)

Why I picked Zoho Books: Zoho offers a full suite of cloud-based services for business and nonprofit organizations. If you’re looking for a one-stop shop for accounting and other key services, Zoho might be the best bet.

Zoho Books Standout Features and Integrations:

Standout features include Zoho Book’s ability to integrate with the company’s other services, including donor management, marketing, HR, legal services, and IT management, making it a potential one-stop shop for admin needs. On its own, the tool offers mileage and expense tracking, the ability to receive payments online and in person, and invoice management services. You can also use its automation tools to import statements from credit cards and bank accounts.

Integrations include other Zoho tools, along with PayPal, Stripe, WePay, and other payment tools.

Price: Pricing upon request

Free Trial: 14 days

  • Try the service out using a test account before you sign up
  • Highly intuitive and easy to use with no experience
  • Free for small nonprofits
  • Free for organizations with annual revenues less than $50,000.
  • Limited support
  • Few customization options

4. ZipBooks - Best for unlimited invoicing

ZipBooks financial performance dashboard screenshot
ZipBooks displays essential financial information through a simple dashboard. (Image Source)

Why I picked ZipBooks: If your nonprofit does a lot of invoicing, ZipBooks is easy to use and one of the cheapest ways to send and track invoices.

ZipBooks Standout Features and Integrations:

Standout features include unlimited invoices, making it one of the top free nonprofit accounting tools. You can accept major payment methods and access mobile accounting tools to track payments. It also has team management tools like time tracking.

Integrations include Google Drive, Square, PayPal, and major banks.

Price: From $15 per month

Free Trial: 30 days

  • Free service is suitable for many smaller nonprofits
  • Higher levels of service are low cost
  • Easy payment acceptance
  • Limited support
  • Few integrations

5. Xero - Best for customization

Xero dashboard screenshot
Xero’s dashboard displays your nonprofit’s payables and receivables, as well as account balances. (Image Source)

Why I picked Xero: Xero offers key tools nonprofits need, plus file storage, tax calculations, and more. Its reporting tool is also highly customizable, letting you build reports that provide the most valuable information for your needs.

Xero Standout Features and Integrations:

Standout features include the ability to build custom reports to track the exact financial data that you need or to generate forecasts. Xero offers key financial services like payment acceptance and the ability to connect to external banks. You can also use it for payroll services and file storage if you want more functionality.

Integrations include third-party banks, Gusto payroll, Shopify, Microsoft Outlook, Stripe, Mailchimp, and more.

Price: From $9.75 per month

Free Trial: 30 days

  • Reporting tools
  • No limit to the number of users on one account
  • File storage for receipts, customer data, etc.
  • 24/7 support
  • Many features require an advanced subscription
  • Some services, like payroll, come at an additional charge

6. QuickBooks - Best for tracking cash flow by project

Quickbooks business overview dashboard
QuickBooks’ dashboard might look complicated, but it displays key details about your nonprofit’s financial accounts and cash flow all in one place. (Image Source)

Why I picked QuickBooks: QuickBooks is one of the best-known accounting tools out there. It has an intuitive user interface and relatively cheap plans that come with most of the key features for nonprofits.

QuickBooks Standout Features and Integrations:

Standout features include budget tracking, expense sorting, and automated reporting. Quickbooks will also let you accept donations through multiple payment methods. If you want HR-related services, it also comes with payroll and time-tracking options.

Integrations include PayPal, Square, SOS Inventory, Gusto, and more than 750 more.

Price: From $15 per month

Free Trial: 30 days

  • Nonprofit-focused compliance and reporting tools
  • Donor management tools
  • Automated reporting features
  • Numerous guides and how-to resources available online
  • Limited number of users
  • Most nonprofit features are only available in higher-cost plans
  • Additional fee for payroll and other services

7. Realm - Best for churches

Realm chart of accounts screenshot
Realm doesn’t have the fanciest dashboard out there, but it comes with a unique focus on churches that can make it a great fit for those organizations. (Image Source)

Why I picked Realm: Realm has a very specific focus on churches and other worship organizations. If you run a church, you’re likely to have better luck finding the features you need and getting support that understands your situation.

Realm Standout Features and Integrations:

Standout features include Realm’s app for pastors and congregants to help people stay connected to their church, register for events, volunteer, and donate, making this a uniquely helpful tool for churches. On the financial side, it offers financial dashboards, donor tracking and management, and donation acceptance tools.

Integrations: Realm is sold as an all-in-one platform.

Price: From $29 per month

Free Trial: Demo available

  • Designed specifically for churches and worship organizations
  • Donor management and tracking capabilities
  • Easy to use
  • 24/7 support
  • Limited features
  • Opaque pricing
  • Not applicable to all nonprofits

8. Wave - Best for ease of use

Wave dashboard screenshot
Wave’s dashboard is simple to read, making it easy to use even for people with limited accounting experience. (Image Source)

Why I picked Wave: If no one in your organization has accounting experience, Wave is one of the easiest-to-use tools on the market. You can set up an account and get running in just a few minutes.

Wave Standout Features and Integrations:

Standout features include connecting your account to an unlimited number of bank accounts and credit cards, invoicing, revenue and expense tracking, and financial reporting. If you have multiple nonprofits, Wave also makes it easy to manage multiple organizations with a single account.

Integrations include anything you can link with Zapier, although that may be somewhat more advanced.

Price: Free. Payments from 2.9% + $0.60

Free Trial: Purchase required

  • Completely free if you don’t use add-on services
  • Custom invoicing
  • Free reporting and expense tracking
  • Restricted funds have to be tracked manually
  • Limited free support

9. Quicken - Best for individually-run nonprofits

Quicken spend dashboard screenshot
Quicken’s dashboard comes with a spending overview feature and transaction tracking that can help you monitor your nonprofit’s spending. (Image Source)

Why I picked Brand: Quicken is a low-cost service that is designed largely for individuals tracking their finances, but it does offer a small business service that works well for small nonprofits with just one or two people involved.

Quicken Standout Features and Integrations:

Standout features included by Quicken make it easy to automate expense tracking using custom spending categories and to use that information with the service’s budgeting and forecasting tools. More advanced users can design custom reports and use what-if analysis to project their financial futures.

Integrations include bank and credit card accounts, and PayPal.

Price: From $3.99 per month

Free Trial: Purchase required

  • Limited features
  • No product demo or free trial offering

10. Serenic Navigator - Best for a range of features

Serenic Navigator dashboard
Serenic Navigator can sort data by department, award or fund, date range or more. (Image Source)

Why I picked Serenic Navigator: Serenic Navigator is purpose-built with nonprofits and other similar organizations in mind. It offers key budgeting and financial tracking tools as well as other useful services.

Serenic Navigator Standout Features and Integrations:

Standout features include a variety of related services like IT and HR services that make it easy to get all your admin help from one place. The accounting tool in particular has reporting tools, core fund accounting, grant and award management, and easy-to-use budgeting tools.

Integrations include Sylogist’s other services, including IT management, web portals, and business apps.

Price: Pricing upon request

Free Trial: Purchase required

  • Designed specifically for nonprofits
  • Wide variety of add-on services
  • Financial tracking and budgeting tools
  • Pricing is not transparent
  • Works best if you buy multiple services, not just accounting

11. NetSuite - Best for enterprise and international nonprofits

Oracle NetSuite dashboard screenshot
NetSuite lets you track important KPIs for your nonprofit through an easy-to-read dashboard. (Image Source)

Why I picked NetSuite: NetSuite is a highly modular program, giving you the flexibility to choose the tools and functionality that your nonprofit needs to succeed.

NetSuite Standout Features and Integrations:

Standout features of NetSuite’s cloud-based tools include a general ledger, cash management, tax compliance tools, as well as payment and donor management.

Integrations include a variety of other NetSuite services.

Price: Pricing upon request.

Free Trial: Free live demo available.

  • Modular tool that lets you select the services you need and forgo the ones you don’t
  • Customizable pricing based on selected services
  • Accounting and reporting tools
  • Pricing lacks transparency
  • The tool can be very complex

12. Sage Intacct - Best for global nonprofits

Sage Inatacct CFO dashboard screenshot
Sage Intacct offers multi-currency support and tracking tools so you can view your nonprofit's performance across borders. (Image Source)

Why I picked Sage Intacct: Sage offers flexible financial management tools and support for a variety of global currencies.

Sage Intacct Standout Features and Integrations:

Standout features include multi-currency support, which makes Sage Intacct the best choice for international nonprofits. It also comes with accounts payable and receivable management, financial reporting tools, expense management, cash flow management, and payroll service.

Integrations include Jira, Paychex, APS Payroll, and more

Price: Pricing upon request.

Free Trial: Free demo available

  • Flexible accounting tool
  • Multi-currency support
  • Many integrations and add-on services
  • Steep learning curve
  • Pricing is not transparent

Other Options

If you don’t feel any options on my list are the right fit for your organization, here are a few other nonprofit accounting tools to consider:

  1. AccuFund - Best for government agencies
  2. UncommonGood - Best for fundraising
  3. NonprofitCore - Best for donor outreach

Selection Criteria For Non-Profit Accounting Tools

I looked at some of the best accounting programs on the market to compare their key features and see how well they serve the needs of nonprofits.

When comparing accounting programs for nonprofit organizations, I looked at the following criteria.

Core Functionality

Nonprofits need to accomplish many of the same bookkeeping tasks as businesses, tracking cash inflows and outflows and producing financial reports.

Any accounting tool for a nonprofit needs these basic bookkeeping options and some tools for nonprofits’ unique needs, like restricted fund tracking.

Key Features

Nonprofits have unique needs compared to businesses, so they should be looking for some specific features and tools.

For example, many nonprofit organizations rely on donations from people in their communities. Donor management is key to tracking these donations and working with people likely to make future donations.

Another key feature is the ability to track restricted funds. If a donor makes a gift with restrictions on how you can use the money, the last thing that you want is to spend that donation improperly or have it mixed with funds that you expect to rely on for other purposes.

Some also offer other unique functions, such as the ability to connect and communicate with volunteers. Nonprofits that rely on volunteers might appreciate being able to use the same app to find people who are willing to help out at different events.

I looked for accounting programs that offered donor management tools and other services focused on the unique needs of nonprofits.


It’s no secret that accounting can be a complicated topic. People spend years in higher education institutions to earn degrees that focus on it. It’s easy for that complexity to spill over into accounting software, leaving you with a tool that requires a textbook to understand.

Accounting software is there to help you manage your finances more easily. The best tools are intuitive and easy to pick up while still having all of the advanced features that you need. Extensive knowledge bases and how-to resources are also a big plus.


Your nonprofit likely relies on a variety of programs and tools to handle different tasks. For example, you might use something like Paypal to accept donations.

Many accounting programs integrate with other financial services to make it easy to import data or track transactions. These integrations can save you a lot of time and help make it easier to track your organization’s finances.

Add-on services such as payroll services

Some accounting programs do more than just let you track your organization’s finances. They may try to serve as an all-in-one financial suite for your nonprofit. That can be a big plus if you’re looking for a single service that does it all.

I looked at accounting tools that have optional services, such as payroll or inventory management, that may help you run your nonprofit more efficiently.


Sometimes, even the best accounting programs can have bugs or be a bit confusing to use. Should your software ever crash or freeze up on you, having reliable technical or customer support you can turn to is critical. I looked for software that has support that is easy to reach and has a reputation for being helpful.

People Also Ask

Here are some common questions and answers about nonprofit accounting software.


Every nonprofit can benefit from having accounting software to fit its purpose. The right program will help you keep track of donations and make sure you’re putting your financial resources to proper use.

The right program can also further your nonprofit's mission by helping you spend less time and money on managing the organization’s finances and more on the people you’re trying to help.

If you want more financial management insight and advice, sign up for our newsletter to get resources and advice from leading experts.

By Simon Litt

Simon Litt is the Editor of The CFO Club, where he shares his passion for all things money-related. Performing research, talking to experts, and calling on his own professional background, he'll be working hard to ensure that The CFO Club is an indispensable resource for anyone seeking to stay informed on the latest financial trends and topics in the world of tech.

Prior to editing this publication, Simon spent years working in, and running his own, investor relations agency, servicing public companies that wanted to reach and connect deeper with their shareholder base. Simon's experience includes constructing comprehensive budgets for IR activities, consulting CEOs & executive teams on best practices for the public markets, and facilitating compliant communications training.