Best Accounting Software for Nonprofits

Find the right tools to track donations and expenses for your organization

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When it comes to accounting software, it's just as important for nonprofits to track income and expenses as it is for businesses. Nonprofits must follow strict guidelines to maintain their tax-exempt status. If they don’t, they can lose this status, which can open them up to an IRS audit and make all of the donations they’ve previously received taxable.

When looking for accounting software, it’s important that it allows for detailed tracking of donations, donors, and expenses. In addition, software should be able to generate detailed reports for presentation to a board of directors and donors, as well as for filing the annual IRS Form 990. 

We looked at about a dozen of the top accounting systems available based on all of these factors and more and identified the best accounting software for nonprofits. These are our top picks.

The 8 Best Accounting Software for Nonprofits of 2022

Best Overall : FastFund Online Nonprofit Fund Accounting



FastFund Online Nonprofit Fund Accounting is an all-in-one accounting, fundraising, and payroll software program. It was designed by nonprofit experts to meet the needs of nonprofit and small governmental agencies. 

There are four plans to choose from. The all-inclusive Premium plan starts at $94 per month and includes fund accounting, fundraising, and payroll tools all in one program. If you don’t need the all-inclusive option, you can purchase just the plans that you need. The fund accounting plan and fundraising plans both start at $42 per month, and the payroll plan starts at $66 per month. There is no setup fee, you can cancel anytime, and technical support is included in all four plans. 

We chose FastFund Online Nonprofit Fund Accounting as the best overall accounting software for nonprofits because it meets the accounting, fundraising, and payroll requirements at the best price, less than $100 per month.

Features of each of the plans offered by FastFund include:

Nonprofit Accounting Plan 

  • Customized chart of accounts
  • FASB-compliant financial statements
  • Reports to assist with completing IRS Form 990
  • Tracking of cash receipts and disbursements
  • Customized financial statements
  • Budgets

Nonprofit Fundraising Plan

  • Constituent management
  • Campaign management
  • Membership management
  • Cash, pledge, in-kind gift processing
  • Automated receipts
  • Pledge reminders
  • Customized reports

Nonprofit Payroll Plan 

  • Payroll payment options
  • Built-in payroll tax tables
  • Automatic payroll tax payments
  • Payroll tax filings
  • Customized reports

You can schedule a free one-hour demo to learn more about how the software works. Tech support includes access to free webinars and YouTube video tutorials, and you also can schedule a private training session for your staff at an hourly rate of $100.

Runner-Up, Best Overall : Aplos



Since 2009, Aplos has provided an accounting software solution nonprofit organizations can rely on to keep track of donors, contributions, and fundraising events. 

Like most of the providers on our list, Aplos is a cloud-based program, which makes it compatible with any computer or mobile device with an Internet connection. We chose Aplos as the runner-up because it includes several features starting at $59 per month.

Aplos Features

  • Fund accounting
  • Donor management
  • Online donations
  • People database
  • Create and manage groups
  • Fundraising tools
  • Event registration
  • Website builder
  • Financial statements
  • Budget reports

Aplos also offers software customized to meet the needs of any church. The advanced accounting upgrade package starts at $159 per month. It includes budgeting by fund or tag; creating reports by project, campaign, or department; creating and sharing giving statements; tracking fixed assets; and a groups and team portal. If you have employees, you can add payroll with Gusto for an additional fee or, if you prefer to outsource your bookkeeping, Aplos offers bookkeeping services.

If you need help, Aplos has online tools as well as telephone, chat, and email support. Sign up for a free 15-day trial to take Aplos for a test drive. Finally, if you dread completing the IRS Form 990, you can purchase software from Aplos that will complete the form for you.

Best Desktop Solution : Intuit QuickBooks Desktop for Nonprofit

Intuit QuickBooks

Intuit QuickBooks

Intuit QuickBooks Desktop is one of the most widely used small business tools ever made, and the Nonprofit edition was created to meet the tracking and reporting needs of nonprofit organizations specifically. 

There are three plans to choose from: the Plus plan, with a monthly payment of $80, the Advanced plan, with a monthly payment of $180, and the Enterprise Nonprofit plan, which is $125 a month. The differences revolve around the number of users, access to premium apps, advanced data and analytics, and access to the latest features and updates. 

We chose Intuit QuickBooks Desktop for Nonprofit as the best desktop solution because Intuit QuickBooks is used by more small businesses than any other software.

Quickbooks Desktop Plan Features

  • Financial reports specific to the nonprofit industry
  • Customized chart of accounts for nonprofit
  • Access for up to five users
  • Track income and expenses
  • Manage bills (accounts payable)
  • Manage outstanding donations (accounts receivable)
  • Budgeting and reporting
  • Recurring donations

Unlike Aplos and QuickBooks Online, these versions of QuickBooks Desktop for Nonprofit must be installed on a Windows computer. QuickBooks Mac 2022 is a separate product available for $349.99 per year for one user, $549.99/year for two users, or $749.99/year for three users.

If you need to backup your data, you can sign up for this service for an additional fee. If you need to pay employees, you can add the payroll service for an additional fee. With the payroll service, you can process paychecks, calculate payroll taxes, and pay and report payroll taxes to all local, state, and federal authorities. Similar to QuickBooks Online, you can generate a report that can be used to complete IRS Form 990.

Best for Bookkeepers and Accountants : Intuit QuickBooks Online

Intuit QuickBooks

Intuit QuickBooks

Unlike Aplos, Intuit QuickBooks Online was not specifically designed for nonprofit organizations, but it can be customized for nonprofits. There are four pricing tiers ranging from $25 to $180 per month. We recommend QuickBooks Online Plus because it includes class and project tracking, which can be used to track funds.

QuickBooks Online Plus starts at $80 per month and includes unlimited telephone and chat support. It is cloud-based and will work on any device with an internet connection. We chose Intuit QuickBooks Online as the best for bookkeepers and accountants because of its versatility and popularity, making it an easy option for nonprofits.

QuickBooks Online Plus Features

  • Track income and expenses
  • Track mileage 
  • Access for up to five users
  • Manage bills (accounts payable)
  • Manage paid donations
  • Manage outstanding donations (accounts receivable)
  • Financial statements
  • Budgeting and reporting
  • Recurring donations
  • Capture & organize receipts 

Basic menu items such as changing “customers” to “donors” can be easily accomplished. Plus, when you select nonprofit as the industry, QuickBooks Online automatically includes a custom chart of accounts. If you have employees, you can add payroll by Gusto to your subscription when you’re ready.

Gusto is an integrated payroll solution that will track employees, process payroll checks, track payroll taxes, and make payroll tax payments all within your QuickBooks Online account. Last but not least, you can generate a report that will assist you in completing IRS Form 990.

Best for Churches : Breeze



Breeze is an affordable, cloud-based software designed specifically for churches. The pricing structure is simple—one plan at $50 per month that includes all available features. Breeze has been on the market since 2014 and services more than 8,000 small and mid-sized churches located all over the United States and Canada. We chose Breeze as best for churches because many of its features are customized to meet the specific needs of houses of worship.

Breeze Features

  • Event management
  • Access to unlimited users
  • Add unlimited people to the database
  • Online and text giving
  • Track donors and gifts
  • Access your data via the mobile app
  • Create member directories
  • Create, email, and text groups
  • Manage event attendance

Like Aplos and QuickBooks Online, Breeze can be used on any computer with an internet connection. If you need assistance, tech support is available by phone or email.

Best for Enterprise-Level Nonprofits : NonProfit Plus

Nonprofit Plus

Nonprofit Plus

NonProfit Plus is ideal for enterprise-level nonprofit organizations such as schools, museums, foundations, hospitals, government agencies, and food banks. It comes in three suites: nonprofit accounting, financial management, and procurement management. All three suites are cloud-based. We chose NonProfit Plus as the best for enterprise-level nonprofits because it has robust features to meet the needs of large nonprofit organizations.

Nonprofit Accounting Suite Features 

  • Fund accounting
  • Restricted funds management
  • Grant management
  • Encumbrance accounting
  • Budget management
  • Donor management
  • Board management
  • Volunteer management
  • Enhanced audit trail

Financial Management Suite Features

  • General ledger
  • Accounts receivable
  • Accounts payable
  • Cash management
  • Currency management
  • Intercompany accounting
  • Recurring revenue management
  • Fixed assets
  • Time & expense management

Procurement Management Suite Features

  • Inventory management
  • Purchase orders
  • Sales orders
  • Requisitions

Similar to FastFund Online Nonprofit Fund Accounting, you can pick and choose the suite that best fits the needs of your nonprofit organization. NonProfit Plus does not include pricing on its website. You can schedule a free product tour to learn more about all of the robust features included in each suite plus consult with a representative who will create a custom quote based on the needs of your nonprofit.

Best for Large Nonprofits and Government Entities : Blackbaud Financial Edge NXT



Founded in 1981, Blackbaud Financial Edge NXT has provided nonprofit tools in fundraising, marketing, fund accounting, and analytics to large nonprofit and government entities. Similar to FastFund Online Nonprofit Fund Accounting and NonProfit Plus, you can pick and choose which tools you need for your nonprofit. The three main modules are Blackbaud Fundraising, Blackbaud Marketing, and Blackbaud Fund Accounting, though they have others for more specific circumstances.

We chose Blackbaud Financial Edge NXT as the best product for large nonprofits and government entities because it has been successfully meeting the needs of these organizations for longer than three decades.

Blackbaud Fundraising Features

  • Fundraising and supporter management tool called Blackbaud eTapestry
  • A fundraising and donor management tool called Blackbaud Raiser’s Edge NXT
  • An extensive fundraising and relationship management tool on the Salesforce management platform called Blackbaud Luminate 
  • Constituent relationship management for large to enterprise-level nonprofit organizations

Blackbaud Marketing Features 

  • An advanced online marketing tool for creating a full engagement experience for your supporters called Blackbaud Luminate Online
  • Integrated multichannel alumni engagement tool called Blackbaud Net Community
  • Simple, smart, cloud-based online fundraising and marketing tool called Blackbaud Online Express
  • Integrated website tailored to the needs of all nonprofit organizations called Blackbaud Website package

Blackbaud Fund Accounting Features 

  • Blackbaud Financial Edge NXT: A complete fund accounting solution for large nonprofits and government entities
  • Blackbaud Donor Central: An online portal providing access to account and grant-making information
  • Blackbaud FIMS: Fully integrated financial management system

Similar to NonProfit Plus, Blackbaud Financial Edge NXT does not include pricing information on its website. However, you can request a demo so a representative can go through each of the solutions available and assist you in selecting the software that will work best for your nonprofit.

Alternative to Intuit QuickBooks Desktop for Nonprofit : MIP Fund Accounting



MIP Fund Accounting has provided accounting solutions since 1990 to nonprofit organizations. MIP Fund Accounting offers a cloud-based software (MIP Cloud) and an option to install the software on a desktop computer (MIP On-Premises).

MIP Cloud is ideal for nonprofits who already are in the cloud or ready to move. If you prefer a web-based user interface, have reliable internet connectivity, support staff in multiple locations, and don’t have full-time IT staff, MIP Cloud is the best solution. MIP On-Premises is just the opposite of MIP Cloud. MIP on-premises is ideal for an organization that requires an on-premises accounting system due to IT policies, have support staff that is primarily co-located, and has in-house or contracted IT staff. 

We chose MIP Fund Accounting as an alternative to QuickBooks Desktop because it is the only other company on our list that offers a desktop solution (MIP On-premises).

MIP Cloud and MIP On-Premises Features

  • General ledger
  • Dashboards
  • Accounts payable
  • Accounts receivable
  • Bank reconciliation
  • Budgeting
  • Payroll
  • Human resources
  • And much more

For more information about how the software works, you can sign up for a live webinar or schedule a free personal product tour. Pricing information from MIP Fund Accounting is not available on the company's website.


What Is Accounting Software for Nonprofits?

Accounting software for nonprofits is a type of accounting software specifically designed for nonprofit organizations. Accounting software for nonprofits helps these organizations manage accounting, bookkeeping, and tax-related matters, which is important because nonprofits must adhere to strict guidelines in order to maintain their tax-exempt status.

In addition to enabling nonprofits to perform income and expense tracking and payroll, the software tracks and accepts donations and even tracks donor lists, receipts, and fundraising events.

How Does Accounting Software for Nonprofits Work?

Accounting software for nonprofits helps nonprofit organizations complete tasks such as tracking income and expenses, storing receipts, and paying employees. It also has automation tools and can be accessed by multiple users in the organization. Once you input data, the software will perform the necessary calculations, save the data, and categorize it for you. Accounting software for nonprofits typically has the ability to accept payments, print checks, and store receipts and lists.

How Is Accounting Software for Nonprofits Different From Accounting Software for Businesses?

Accounting software for nonprofits is different from business accounting software because the IRS has established certain reporting requirements that nonprofits must meet. For example, IRS Form 990 must be filled out and filed by nonprofit organizations annually.

As such, the reports that are generated using accounting software for nonprofits must include all the information required to complete that form. Nonprofits also need software features that businesses don’t need, such as donation portals, the ability to maintain donor lists, and fundraising tools.

How We Chose the Best Accounting Software for Nonprofits

We research and review each product or service before we recommend it. We reviewed more than a dozen accounting software for nonprofits before choosing the top eight. We reviewed them based on detailed reports, donation-tracking functions, pricing, and tax form preparation. We also considered what additional tools the software offered and the different plans available.

Article Sources

  1. IRS. "Annual Filing and Forms." Accessed Oct. 27, 2021.