As your nonprofit grows, you need to ensure that your bookkeeping department can scale with it. That’s why it’s so crucial for you use technology to your advantage.

Every business should be using accounting software. This holds true whether you’re managing the books on your own, have an in-house bookkeeper, or use an outsourced bookkeeping service.

But nonprofits are unique. There are specific features, functions, and capabilities that you need your bookkeeping software to accommodate.

Rather than just using any accounting solution, you should find software that’s specifically designed for nonprofits.

As someone who has decades of experience in the nonprofit bookkeeping industry, I’ve identified the five best nonprofit accounting software options on the market today. I’ll give you an in-depth review of each one below so you can find the best choice for your nonprofit organization.

1. QuickBooks

QuickBooks is a global leader in accounting software. QuickBooks Desktop and QuickBooks Online both ranked high on my list of the best cloud-based accounting solutions for small businesses. 7+ million companies around the world use this software.

Most people may not realize it, but QuickBooks offers industry-specific solutions—including QuickBooks for Nonprofit.

QuickBooks has everything you need to manage both basic and advanced accounting tasks. It also offers features that will accommodate your needs as a nonprofit.

You can use this software to easily track and accept donations from any source, including credit cards, debit cards, cash, check, or bank transfers. Use the app to record a new donation in real-time.

QuickBooks integrates with third-party apps that you’re already using to collect donations, like DonorPerfect or Fundly.

For both large and small nonprofits, QuickBooks makes it easy for you to generate reports. You can also create specialized reports for board members and donors. Use QuickBooks to automatically email something like a cash flow report to specific people on a monthly or quarterly basis.

  • QuickBooks Online Plus — $70 per month
  • QuickBooks Online Advanced — $150 per month
  • QuickBooks Desktop Premier Edition — $499.95 one-time cost
  • QuickBooks Desktop Enterprise Nonprofit — $1,155 per month

Online plans are available for 50% off your first three months. The desktop Enterprise Nonprofit solution is offered at 10% off the first year. QuickBooks has additional discounts for nonprofits on TechSoup.

2. Aplos

Aplos accounting software was not made for just any business. It’s specifically designed for churches and nonprofit organizations.

This solution is more than just traditional bookkeeping software. It’s a full suite of products and technology that can be used to manage your nonprofit.

Aplos has a nonprofit CRM that helps you create and manage your donors. It’s easy for you to create custom mobile-friendly donation forms and set up recurring and automated tithes. The software will also track tax-deductible gifts from your donors. This makes it easy for you to quickly prepare monthly, quarterly, or annual statements for anyone who donates.

You’ll also benefit from tools that enhance your fundraising campaigns.

For those of you who are just starting out and still growing your nonprofit organization, Aplos even has a nonprofit website builder.

From managing donors to collecting donations, tracking funds, and creating essential financial reports, Aplos does it all.

  • Aplos Suite — $29.50 per month
  • Aplos Advanced Accounting — Custom pricing

Save an additional 10% on your software with an annual subscription.

3. Nonprofit Plus

As the name clearly indicates, Nonprofit Plus is another accounting solution made solely for nonprofits. Common nonprofit industries that use Nonprofit Plus include museums, hospitals, churches, food banks, government, housing, and foundations.

If your organization falls into one of these categories, the Nonprofit Plus Accounting Suite should be a top consideration for your nonprofit bookkeeping software.

This accounting solution has features and functions for things like:

  • Grant management
  • Board management
  • Donor management
  • Restricted funds management
  • Fund accounting
  • Encumbrance accounting
  • Volunteer management

Nonprofit Plus also has tools to enhance your audit trail. The software makes it easy to track all incoming and outgoing cash flow.

Depending on your specific type of nonprofit, the Nonprofit Plus Accounting Suite has additional features to meet your needs.

For example, if you run a food bank, you can benefit from warehouse tools like inventory management and handheld barcode scanners. Nonprofit housing companies can manage monthly rent, set up accounts for multiple properties, and automate calculations for subsidies.

Nonprofit Plus bookkeeping software includes built-in payroll functionality as well. It also integrates with third-party payroll providers.

Pricing for Nonprofit Plus is not available online. You’ll need to contact their sales team for more information about a custom solution for your organization.

4. Xero

Xero is one of the world’s most popular accounting solutions. It’s used by more than two million businesses across the globe.

Unlike some of the other options on our list, Xero does not have specific solutions for nonprofits. However, it does have plenty of tools that your nonprofit organization can benefit from using.

You can easily share information related to donations and expenses with your donors, volunteers, and board members. Xero integrates with more 800+ third-party apps. It will sync with other tools you’re already using for managing donors, fundraising, marketing, and more.

The Xero accounting dashboard is one of the best that you’ll find on the market today. It’s easy for anyone to use and navigate, regardless of your experience with nonprofit bookkeeping software.

Integrate Xero with payment providers like Stripe and PayPal to get paid faster and automatically update your books.

Like everything else offered on this platform, the Xero mobile app is second to none. This tool makes it easy for you to manage your finances from anywhere, which is crucial for nonprofit organizations.

  • Xero Early — $9 per month
  • Xero Growing — $30 per month
  • Xero Established — $60 per month

All plans are available for a 30-day free trial.

Again, Xero does not have nonprofit-specific software. However, registered nonprofit organizations will benefit from 25% off one of the world’s most popular bookkeeping solutions.

5. Sage Intacct

Sage Intacct has an excellent reputation for quality and customer satisfaction for accounting software. Sage Intacct Cloud for Nonprofits is an excellent choice for the following types of organizations:

  • Community improvement nonprofits
  • Human services organizations
  • International nonprofits and NGOs
  • Nonprofit healthcare companies
  • Faith-based nonprofits
  • Educational nonprofits
  • Membership organizations
  • Philanthropic organizations

If you quickly browse through the Sage Intacct website, you’ll find plenty of success stories and case studies of how this software helped various nonprofits.

I’d recommend Sage Intacct to larger nonprofit organizations. The bookkeeping software has tools for managing multiple entities, various grants and donors, and numerous currencies across all your locations.

Contact the sales team for a custom quote on nonprofit bookkeeping software. Ask about special pricing for your organization.


Nonprofit organizations should be using modern and updated accounting software that’s made specifically for nonprofits. If you’re in the market for an updated solution, the five options above will be the best place to start your search.

In addition to using the right accounting tools, you should also make sure you’re working with a bookkeeper that understands and has experience with nonprofits.

Here at Navitance, we specialize in nonprofit bookkeeping and accounting. Contact us today for a free consultation. We can even assist you in choosing the right nonprofit accounting tools.