Best Low-Cost Nonprofit Accounting Software

How to Get Organized Fast

Cash Accounts versus Margin Accounts
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Table of Contents
Table of Contents

Every nonprofit, large or small, can become more organized with accounting software. Nonprofits need reliable accounting software that can keep up with their donations, reports, and budgets with accuracy. Investing in robust accounting software can save you valuable time and energy, as well as improve the efficiency of your nonprofit.

To help you find the right software for your nonprofit, we’ve created a list of five of the best low-cost nonprofit accounting software options available today. To compile this list, we took into account what each low-cost nonprofit accounting software offers, its pricing, and its nonprofit-specific capabilities.

Of course, there are countless nonprofit accounting options out there, so don’t be afraid to play around with demos and free trials to find what is best for you.


Aplos is a web-based accounting software created with nonprofits in mind. It is highly customizable with a user-friendly interface and dedicated to keeping all your receipts and reports in one place. Aplos comes with core features that include budgeting, donor management, and online donation support. It also provides tax support for 1099s and 990s, taking the stress of paperwork off your hands. Aplos can come in handy for smaller nonprofits in need of budget organization, as well as expense tracking and fundraising.

While Aplos offers a range of solutions, it may be best suited for smaller nonprofits, as the features can be too simple to keep up with the processes and demands of a larger organization.

Aplos is ideal for organizations who will not need many users, as the basic plan only allows for one. You can add extra users but that could get expensive if you have many users. Aplos offers a 14-day free trial for nonprofits and churches, as well as on-demand resources and support. 

Aplos core features:

  • Donor management
  • Fund accounting
  • Member management
  • Fundraising tools
  • Online donations & giving
  • Marketing & communication
  • Event registration
  • Reporting & analytics


  • $24/month
  • $18/additional user

Intuit QuickBooks

Intuit QuickBooks is a well-established company with an array of accounting solutions for many industries, including nonprofits. QuickBooks can be a great accounting software choice for nonprofits of any size, with low monthly costs and easy-to-use budgeting tools. QuickBooks syncs with your bank account and offers app integration for PayPal and Square accounts. One popular option is QuickBooks Online, which is affordable and can handle smaller nonprofit operations with ease. QuickBooks also offers Enterprise software that has many features designed for larger nonprofits, but it is more expensive and may be better suited for a dedicated accounting team.

While QuickBooks can be a great low-cost solution for nonprofit accounting, it does come with limitations. The more basic plans, such as Online Essentials, lacks industry-specific tools and limits the number of allowed users. The ability to create and manage budgets is also blocked to lower-level users unless they upgrade their plan to Plus. Some users have also reported file-size issues as well as occasional crashes.

Intuit offers a 30-day free trial of QuickBooks with nonprofit-specific resources and expert support available with every subscription.

QuickBooks core features:

  • Track income and expenses
  • Download bank and credit card transactions
  • Payroll service
  • Reports
  • Online payments service
  • Check printing
  • Various pricing plans


Xero is a simple online accounting software with helpful tools for invoicing, bill management, and standard reports. Xero’s software also syncs with third-party apps for fundraising and donor management, as well as integration with Office 365. It offers three plan options to fit any nonprofit: Early, Growing, and Established. Xero’s plans can be upgraded with increasing access to features such as project tracking and capturing expenses as the nonprofit grows.

Xero can be incredibly useful software, but it does have disadvantages. Some users find the tracking capability challenging to manage, especially for larger organizations that have more complex grants or funds to track. Xero is better suited for small nonprofits who do not need to manage multiple funds or projects. While it may not be the ideal choice for more complex needs, Xero does offer solid nonprofit accounting support while staying affordable. Xero provides a free 30-day trial that does not require a credit card.

Xero core features:

  • Contacts
  • Invoicing
  • Inventory
  • Payroll
  • Financial reporting
  • Free unlimited email support
  • Mobile apps (Android, iPhone/iPad)
  • Purchase orders
  • Quick and easy 1099s


  • Early - $9/month
  • Growing - $30/month
  • Established - $60/month

Araize FastFund

FastFund is online accounting software designed by Certified Public Accountants for nonprofit organizations. It is one of the most affordable options with a wide range of features, free webinars, and integration with Microsoft Office products. FastFund also integrates with accounts payable and receivable, as well as fundraising and payroll. Aside from the cost, the main appeal of FastFund is the easy-to-navigate dashboard that doesn’t require much training. Users like FastFund’s fundraising capabilities and budgeting features, as well as the payroll system.

Araize’s FastFund software is highly rated and offers many useful features, but it does have a few drawbacks. Some users have noted that data entry is not as intuitive as other accounting software. They have also found occasional issues with reporting, which can be difficult to customize. Users also ask for more flexibility when it comes to reports and data for organizations with more complex operations. Araize offers a free 30-day trial of FastFund that can be canceled at any time.

FastFund core features:

  • Customized chart of accounts
  • FASB-compliant financial statements
  • Cash receipts and disbursements
  • Automated recurring entries
  • Data import
  • Multiple budgets
  • Export to Excel, PDF, and other formats


  • Standard - $38/month
  • Premium - $85/month
  • “Add-ons” for accounts receivable, accounts payable, and multi-user capability - $17/ea.

Zoho Books

Zoho Books is an extremely affordable online accounting software with customization and free add-ons. While Zoho Books was not created solely for nonprofits, it does include many features useful for managing donors and funds. There are three monthly subscription options to fit a variety of organization sizes and needs. Since Zoho Books is cloud-based, nonprofits can access their dashboards on any iOS, Windows, or Android device. There are many free add-ons for Zoho Books that users can install for help with specific tasks, such asdonor management, a volunteer portal, and online donations.

Zoho Books is easy to use, but it’s not perfect. Some users have noted difficulty during initial setup. Other complaints included issues with importing spreadsheets and occasional problems with syncing to a bank account. While Zoho Books can be a highly personalized accounting software for nonprofits, it does not support many customizations for reports or automation. Despite a few glitches, many users have found it to be a valuable and affordable addition to their systems. Zoho Books offers a free 14-day trial of their software with free support available.

Zoho Books core features:

  • Invoicing, expenses, and estimates
  • Bill tracking
  • Optimized reporting
  • Purchase orders and sales tax
  • Online payments and vendor credits
  • Multiple project management
  • Bank reconciliations


  • Basic - $9/month
  • Standard - $19/month
  • Professional - $29/month
  • Additional users - $2/user/month

After reviewing options for nonprofit accounting software, many nonprofit boards and decision-makers may feel that hiring a nonprofit accountant is easier. If your organization needs extensive financial reporting, reconciliation, and tracking, a nonprofit accountant may be right for you.

Accountants are an excellent resource for any nonprofit; they can help prepare taxes, advise spending, and reduce financial admin workload for the team. At the end of the day, though, many accountants will need software to help them do their work effectively. Whether you’re a small organization trying to find tools to make your life easier, or your accountant wants a system to support his or her work, nonprofit accounting software may be something you need to improve operations.