The 8 Best Accounting Software for Nonprofits of 2020

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, or 501(c)(3), 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 the software allows for detailed tracking of donations, donors, and expenses. In addition, software should be able to generate detailed reports for presentation to the 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 2020

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 starts at $42 per month, the fundraising plan starts at $20 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, under $100 per month.

Here are some features of each of the plans offered by FastFund:

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
  • Comprehensive 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. Access to a demo file for 30 days is also available. Tech support includes access to free webinars, YouTube video tutorials, and you can also 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 at a very affordable price, 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 a church software customized to meet the needs of any house of worship. The advanced accounting upgrade package starts at $150 per month. It includes budgeting by fund or tag; creating reports by project, campaign, or department; creating custom role permissions; tracking fixed assets; and managing multiple entities. 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 two plans to choose from: The Premier 2020 plan, with a one-time payment of $499.95, and the Premier 2020 Plus plan, which is a subscription-based plan starting at $499.95 per year. The primary difference between the two is that the Premier Plus plan includes unlimited customer support, automatic data backup and recovery, 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 and it is affordable.

Quickbooks Desktop Premier 2020 and Premier 2020 Plus 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, QuickBooks Desktop for Nonprofit must be installed on a Windows computer; it is not compatible with Mac. In addition, it is only accessible on the computer where the software has been installed. 

If you need to remotely access your data, you can sign up for cloud-access which will involve 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 between $20 to $150 per month. We recommend QuickBooks Online Plus because it includes class and project tracking, which can be used to track funds. QuickBooks Online (QBO) Plus starts at $70 per month and includes unlimited telephone and chat support. QBO 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 nine out of 10 bookkeepers use Intuit QuickBooks Online to support their small business clients.

QuickBooks Online Plus Features

  • Track income and expenses
  • Track mileage 
  • Access for up to five users and two accountants
  • 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 easily be accomplished. Plus, when you select nonprofit as the industry, QBO will automatically include 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. They service more than 7,000 small and mid-sized churches located all over the United States and Canada. We chose Breeze as best for churches because many of their 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 and share member directories
  • Create, email, and text groups
  • Manage event attendance

Like Aplos and QBO, Breeze can be used on any computer with an internet connection. If you need assistance, tech support is available by phone or email. You can sign up for a free 30-day demo to determine if Breeze is right for your church.

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. NonProfit Plus comes in three suites: nonprofit accounting, financial management, and procurement management. All three suites are cloud-based, accessible via a mobile app, and allow for unlimited users. 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. While NonProfit Plus does not include pricing on its website, we found the starting price range is between $585 and $975 per month. 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 1983, 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 modules are Blackbaud Fundraising, Blackbaud Marketing, and Blackbaud Fund Accounting. 

We chose Blackbaud Financial Edge NXT as the best product for large nonprofits and government entities because they have been successfully meeting the needs of these organizations for over 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 CRM 
  • 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 their website. However, you can request a demo so that 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 for more than 30 years to nonprofit organizations. Unlike the other providers on our list, 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 are already 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 are primarily co-located, and have 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

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.

In order for nonprofits to maintain their tax-exempt status and meet the reporting requirements of stakeholders like their board of directors, donors, and the IRS, selecting the right accounting software is key. At a minimum, the software should be able to track donations, donors, and expenses by fund. In addition, you should have access to detailed reports in order to meet the reporting requirements of state, local, and federal tax authorities. Otherwise, you could be subject to an IRS audit and potentially lose your 501(c)(3) status.

What Is Accounting Software for Nonprofits?

Accounting software for nonprofits allows for detailed tracking of donations, donors, and expenses incurred by the nonprofit, at a minimum. Nonprofits must adhere to strict guidelines set by the Internal Revenue Service for 501(c)(3) organizations. As a result, the reports that are generated using accounting software should include all of the information required to complete IRS Form 990, which must be filed by all nonprofit organizations annually

Why Do Nonprofits Need Accounting Software?

Similar to for-profit businesses, nonprofit businesses need to keep track of their day-to-day business transactions. This includes donations received and expenses incurred. Since nonprofits must follow strict guidelines when it comes to how the donations they receive are used, accounting software is a necessity so that donations and expenses can be tracked by fund. One of the benefits of using accounting software is all of the data entered is used to generate detailed financial statements. These financial statements can be shared with stakeholders such as the board of directors and donors. In addition, these reports are also used to file federal, state, and local forms as needed.

How Much Does Accounting Software Cost?

Based on our research, accounting software can be purchased on a subscription basis for as little as $42 per month or more. Intuit QuickBooks Desktop for Nonprofit is one of two products for which you can pay a one-time fee, starting at $399. Instead of being cloud-based, the software must be installed on a desktop computer. Most of the accounting software for nonprofits include tracking of donations and donors, custom chart of accounts, tracking of income and expenses, budgeting, and detailed reports. Upgrades to the basic features include fundraising tools like campaign management and pledge reminders, online marketing tools, time and expense management, and inventory management, to name a few. In general, most providers offer an all-inclusive package or you can pick and choose the plans that best meet your needs.

How Is Software Different for Nonprofits?

Nonprofit organizations can use the same software for-profit businesses use. However, they need to make sure that the software can be customized for a nonprofit. Intuit QuickBooks Online is an example of accounting software designed for any type of business that can be customized to meet the needs of nonprofits. Accounting software designed specifically for nonprofits, like Aplos, will automatically include a custom chart of accounts and custom reports for nonprofits. In addition, it may include other features such as fundraising tools, event registration, and the ability to manage donors and accept online donations. 

How We Chose the Best Accounting Software for Nonprofits

We chose the best accounting software for nonprofits by looking at a total of 10 providers, comparing the products' affordability, tracking of donors and donations, detailed income and expense tracking by fund, and detailed financial reports that could assist in the completion of the annual filing of IRS Form 990. We also considered the availability of support, the ability to customize and expand the product offerings, as well as company history and user experience to select the best accounting software for nonprofits.