The 6 Best Nonprofit Accounting Software

We are driven by the Fit Small Business mission to provide you with the best answers to your small business questions—allowing you to choose the right accounting solution for your needs. Our meticulous evaluation process makes us a trustworthy source for accounting software insights. We don’t just scratch the surface; we immerse ourselves in every platform we review by exploring the features down to the finest nuances.

For our roundup of church accounting software, we created a special rubric that evaluates the features of our chosen providers, which gives our audience—churches and faith-based groups—an unbiased opinion about the software’s capabilities and fit for your organization.

All plans include two users:

• Aplos Lite: $79 per month
• Aplos Core: $99 per month
• Aplos Advanced: Starting at $189 per month

Price per additional user is $20 per month.

You can try Aplos for free for 15 days with no credit card required.

Aplos is our overall best nonprofit accounting software because it has an outstanding set of general accounting features, and its key features are tailored to nonprofit operations. We consider it a powerful accounting application for medium-sized nonprofits because it provides end-to-end solutions for managing donors and members.

We recommend Aplos Core for its valuable features, such as fund accounting, donation tracking, and online giving forms. It is also ideal for faith-based organizations with few employees; see how it benefits churches in our evaluation of the best church accounting software.

In our evaluation, Aplos performed well in both accounting and nonprofit features. We did dock a few points in the accounting category because of the added cost for payroll, the lack of inventory features, and no mobile app. That said, these missing features aren’t major drawbacks, and Aplos is still a strong choice. Its ease of use really stands out, with multiple customer service channels that make it simple for users to get help when they need it.

While Aplos is our top overall pick, you may want to consider QuickBooks Enterprise Nonprofit Edition as an alternative. Although Aplos performs well in accounting, QuickBooks Enterprise edges ahead with its dedicated nonprofit edition, offering more tailored features for nonprofit organizations. QuickBooks Enterprise has more accounting capabilities such as class and location tracking, customized reporting, a meticulous A/P and A/R process, and detailed inventory management features.

Prices aren’t published on its website. You can sign up for a free product tour to see how it works.

We selected NonProfit+ by Acumatica as one of the best nonprofit accounting software because it efficiently tracks restricted funds, making it easy for nonprofits to account for transactions affecting restricted donations or grants. It also lets you generate customized reports by activity and schedule emails to send out to donors.

Nonprofit+ is the only software in this category to earn perfect marks in nonprofit accounting. It stands out for its nonprofit-specific features, offering a wide range of tools like fund accounting, grant management, and member management.

While it performed well in accounting, we deducted points for the added cost of payroll, the lack of inventory features, and the absence of receipt scanning. Nonprofit+ also falls short in terms of ease of use. We found the software to be somewhat complex and lacking in assisted bookkeeping features, which could be a drawback for some users.

Aplos is our top alternative to Nonprofit+ for those who find the latter too complex for their needs. Aplos strikes a good balance between accounting and nonprofit features, making it an ideal choice for the average user looking for simplicity without sacrificing functionality.

• Simple Start: $35 per month for one user
• Essentials: $65 per month for three users
• Plus: $99 per month for five users (recommended for nonprofits)
• Advanced: $235 per month for 25 users

QuickBooks currently offers a 50% discount for the first three months or a 30-day free trial with no credit card required.

As our best small business accounting software, QuickBooks Online is a versatile and flexible accounting solution that can adapt to a nonprofit—we have a guide on how to set up QuickBooks Online for nonprofits. We’ll show you exactly how to customize your Q uickBooks Online so that all the necessary information for your Form 990 can easily be printed. From modifying your chart of accounts to perfectly match the Form 990, to using class and location tracking to group revenue and expenses by program service, QuickBooks is incredibly flexible.

It also made our roundup because of its outstanding bookkeeping assistance available through QuickBooks Live. In addition to QuickBooks Live, you can easily find a QuickBooks ProAdvisor in your area to provide you with assistance. You can even give them direct access to your books so they can keep them clean and up-to-date.

We recommend the Plus plan because of the location and class tracking features, which can be used to monitor income and expense by program service, administrative, and fundraising purposes. However, Advanced is also an excellent choice if you require more than five users.

QuickBooks Online performed well in accounting features, though we deducted a few points because some aspects need to be manually adjusted for nonprofit accounting, such as updating the chart of accounts to include nonprofit-specific accounts. However, it excelled in ease of use because of its multiple customer support channels and assisted bookkeeping services.

On the downside, QBO didn’t score highly in nonprofit-specific features. We reduced points because many essential functions, like donation tracking, require manual modifications to meet nonprofit needs. Our best alternative for QBO would be QuickBooks Enterprise if you want nonprofit accounting functions built-in to the software.

All prices above are for one user. Additional users can be added for a discounted price compared with the initial user.

QuickBooks Enterprise is a robust desktop accounting software that is the sole remaining QuickBooks Desktop product following the recent retirement of QuickBooks Desktop Premier. In our view, Enterprise offers more power and functionality than Premier. Like Premier, it includes industry-specific editions, but now with both cloud-hosted and desktop versions available. We appreciate that QuickBooks provides businesses the flexibility to either access Enterprise remotely via cloud hosting or stick with the traditional desktop setup.

As QuickBooks’ most advanced accounting solution, Enterprise doesn’t hold back on features. It supports managing donations, grants, and encumbrances and simplifies tax reporting with IRS Form 990. With QuickBooks Desktop now subscription-based, users benefit from continuous access to the latest updates—something that wasn’t possible with the old license-based version, where updates were limited until the license expired.

QuickBooks Enterprise excels in accounting features, but it does have some drawbacks. In our evaluation, it lost points for not offering a mobile app, missing receipt capture, and charging extra for payroll. However, its nonprofit-specific edition helps make up for these gaps, making it a strong choice for nonprofits overall.

That said, as an accounting-focused software, QuickBooks Enterprise doesn’t include certain nonprofit-specific features like member management. Additionally, its pricing can be high, especially for smaller, grassroots nonprofits. For a more affordable option that still delivers essential features, QuickBooks Online could be a better fit. Alternatively, Aplos provides a solid balance between accounting and nonprofit tools.

You can choose from two plans:

• Starter: Free for a single user; has accounting and invoicing features
• Pro: $16 monthly or $170 annually for unlimited users; has additional features, including bank feeds, receipt capture, live chat and email support, and discounted credit card processing fees

Add-ons:

• Bookkeeping support: $149 monthly (Starter and Pro)
• Assisted payroll: $40 monthly for tax service states and $20 monthly for self-service states, plus $6 monthly per employee
• Receipt scanning: $8 per month or $72 per year (Starter only; included in Pro)

Nonprofits with less than $50,000 in gross receipts can file Form 990-N instead of Form 990, which means they don’t have to separate expenses into administrative, program service, and fundraising. Wave’s basic accounting features will work great for these small nonprofits. Wave doesn’t offer industry-specific features, but small nonprofits most likely won’t need them.

The platform is user-friendly, even for novice treasurers, and personalized coaching is available through a Wave Advisor if needed. However, unlike QuickBooks Online, Wave cannot separate income and expenses by classes to simulate fund or program service accounting as required for Form 990. If you’re required to file Form 990, investing in a more robust solution like QuickBooks Online would be a better fit.

Wave stands out as a leader in pricing, even with its paid option. For just $16, you gain added convenience with features like automated transaction imports. However, the free version still offers all the essential bookkeeping tools. Given that Wave is free, it’s understandable that its accounting score doesn’t match more comprehensive platforms like QuickBooks Online.

Additionally, Wave lacks nonprofit-specific features, so if you require fund tracking or grant management, you may need to consider other options. That said, Wave’s simplicity makes it a solid choice for basic tracking needs. If you’re looking for more robust nonprofit and accounting functionality, Aplos or QuickBooks Online would be worth exploring.

Prices aren’t published on the website, but you can contact the provider to request pricing information or a customized quote.

Blackbaud Financial Edge NXT is comprehensive for tracking both simple and complex grant requirements. Since it’s a nonprofit ERP software, you can specify how your financial data looks on reports and break your accounting structure down to a very detailed level if required.

The program is also ideal for organizations that require consolidated reporting, thanks to its consolidation management module, which allows users to merge financial statements across multiple organizations. On the downside, it lacks transparent pricing, is complex, and requires a lot of training and support to get up to speed on the basic functionality. Aplos might be a simpler and more convenient alternative for nonprofits not leaning toward ERP functions.

Blackbaud earned the second-highest score in nonprofit features, largely because of its status as a nonprofit ERP. The only reason it didn’t receive perfect marks is the absence of member management features. That said, it performed well in accounting, with only minor misses like receipt capture and mobile app functionality. In our expert opinion, the benefits of Blackbaud being an ERP outweigh the lack of these minor features.

Blackbaud’s pricing is likely higher, as is common with most ERPs. However, the exact cost is unclear because it’s quote-based. Additionally, we found Blackbaud more complex to use, which led us to deduct points for ease of use. If you feel an ERP is more than you need, QuickBooks Enterprise might be a more suitable alternative.