Top 10 Best Accounting Software for Nonprofits (Free & Paid)

Last Updated:Wednesday, February 14, 2024

Quick Summary:

From basic to advanced features, accounting software for nonprofits is designed to streamline financial management, enhance transparency, and support the specific reporting requirements of nonprofits. Whether you're looking to upgrade from a simple accounting tool or seeking a more sophisticated system, our article will help you find the perfect fit for your organization's needs.

Are you a small nonprofit that wants to move beyond Google and Excel spreadsheets for tracking expenses? Or maybe you’re a growing nonprofit organization that deals with hundreds of donors and volunteers and needs a solution that will improve its efficiency. 

That’s where our review of the best accounting software for nonprofits comes in! Whatever the size of your organization and your specific needs, there’s an accounting software that can solve your accounting and bookkeeping headaches. 

We made a list of the 10 best accounting software for nonprofits. Some of the accounting software options would be more suitable for smaller organizations and others for large-scale nonprofits with more complex needs. 


Best Software for Nonprofit Accounting Comparison Chart (Top 10 Highest Rated Nonprofit Accounting Systems)

According to nonprofit accounting software reviews and our own extensive research, these 10 options surfaced as the best options for 2024. Let’s briefly compare each accounting system for nonprofits in terms of pricing and what it’s best for:


Best for




Best overall 


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Quickbooks Online


$30/month; discounts for nonprofits available via TechSoup

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Wave Accounting

Free option


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Sage Intacct

Nonprofits with multiple locations 

Pricing is not publicly available

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Growing nonprofit organizations 

$12/month; 25% discount for nonprofits 

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Zoho Books 

Nonprofits on a budget

$20/month;  15% off for nonprofits 

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Blackbaud Financial Edge NXT

Large organizations 

Pricing is not publicly available

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Software 4 Nonprofits (Accounts)

Small nonprofits

$95 per year

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Money Minder

Volunteer-led organizations 

Free plan; $179/year

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Expense tracking 

$15/month; discount for nonprofits available 

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What is the Best Accounting Software for Nonprofits? Here’s Our Top 10 List:

Here, we'll explain the best accounting software for nonprofits and discuss the top features and functionality, pricing plans, and the pros and cons of each software. Some options would be better suited for smaller nonprofits with basic needs and others for growing organizations with many moving parts. 

1. Aplos (Best Accounting Software for Nonprofit Organizations Overall)

aplos accounting software

Why We Chose It:

We chose Aplos as the top accounting software for nonprofits, recognizing its specialized design for nonprofit and church management. This software shines for medium-sized organizations, packed with features like donor and event management, CRM, and a website builder tailored for online fundraising.

We particularly appreciate its dynamic CRM, which efficiently tracks and engages with members and donors. Aplos also offers us over 70 types of financial reports, making organizational performance assessment straightforward.

Additionally, its Advanced Accounting plan is a game-changer, enabling budgeting by fund, fixed asset tracking, and simplifying IRS Form 990 completion.

We believe these robust capabilities firmly establish Aplos not only as an exceptional choice for church accounting but also as a standout in the nonprofit software arena.


  • Trusted by 40,000+ nonprofits and churches

  • 10% off with an annual subscription

  • 15-day free trial 

  • Specifically designed for nonprofits and churches

  • Includes tools to build and host your website

  • Accepts donations via text

  • Free email and phone support

  • Event registration and donor management tools

  • Tax forms


  • Lacks a mobile app

  • Adding additional users requires a fee

  • Doesn’t include built-in payroll 


  • Aplos Lite, $39.50/mo

  • Aplos Core+, $69.50/mo

  • Aplos Core and Advanced Accounting, custom pricing

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Go to Aplos’ official website


2. Quickbooks Online (Most User-Friendly Online Nonprofit Accounting Software)

quickbooks dashboard

Why We Chose It:

We selected QuickBooks Online as the most user-friendly online accounting software for nonprofits on our list, even though it's not exclusively designed for this sector. Its versatility shines in its adaptability to the unique requirements of small nonprofit organizations.

We find its user-friendliness particularly appealing, especially for those new to accounting.

In our experience, the Plus plan of QuickBooks Online is advantageous, offering features like location and class tracking, which are essential for segregating activities by fund and program service.

For larger needs, we recommend the Advanced plan, accommodating more than five users. Also, the QuickBooks Enterprise Nonprofit plan is worth checking out, as it is ideal for larger organizations, with specialized features like donation and church management and a tailored nonprofit chart of accounts.

While QuickBooks Online offers user-friendliness and adaptability, Aplos, our top pick, provides a more tailored experience specifically for nonprofits and churches, with a suite of features directly catering to their unique financial management needs.


  • Trusted by thousands of nonprofit organizations

  • Various monthly plans to choose from

  • Generous accounting features

  • Integrates seamlessly with other Intuit products 

  • 50% discount for the first three months

  • Comprehensive mobile app 

  • Can be tailored to fit nonprofit operations

  • Large knowledge base with help articles and webinars 


  • Lacks nonprofit-specific features

  • Payroll comes at an additional cost

  • The Simple Start plan only supports one user


  • Simple Start: $30 /month

  • Essentials: $55 /month 

  • Plus: $85 /month

  • Advanced: $200 /month 

QuickBooks Online review

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Go to QuickBooks’ official website


3. Wave Accounting (Good Free Accounting Software for Nonprofits)

wave accounting

Why We Chose It:

We voted Wave Accounting as a good free option for nonprofit accounting, valued for its cost-effectiveness and user-friendly interface.

Ideal for small nonprofits, Wave offers essential functions like invoicing and receipt scanning without subscription fees. Its basic financial reporting tools are suitable for small organizations managing donations and expenses.

Wave's strengths lie in its invoicing and receipt scanning capabilities, which are particularly useful for nonprofits that need to manage donations and expenses meticulously. Additionally, its basic financial reporting tools provide sufficient insights for small organizations to keep track of their financial health.

When compared to Aplos, our top pick, Wave serves well for fundamental accounting needs at no cost, but lacks the specialized features for nonprofits that Aplos provides.

If you’re not sure whether Wave Accounting is what you need, but you’d like free or cost-effective solutions, check out our list of best open source accounting software currently available.


  • Easy to use

  • Free forever

  • Great for small nonprofits


  • Not a good fit for large nonprofits

  • Lacks nonprofit-specific features


  • Free 

Wave review

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Go to Wave’s official website​


4. Sage Intacct (Great Budgeting Software for Nonprofits with Multiple Locations)

sage intacct accounting software

Why We Chose It:

Sage Intacct comes equipped with all the features nonprofits need to save time doing administrative tasks so they can focus on more important matters. For instance, this nonprofit budgeting software lets you automate fund, grant, revenue, and billing processes. 

Its strengths include handling complex financial tasks and multi-entity global consolidations, ideal for larger nonprofits. Additionally, Sage Intacct's real-time reporting tools provide critical insights for effective program and resource planning.

Compared to other software like Aplos, Sage Intacct excels in managing intricate financial scenarios and offering comprehensive insights, making it highly suitable for larger, multi-site nonprofit organizations.

In addition, the software’s advanced real-time reporting capabilities let nonprofits check how well their organization is performing and better plan for programs, fundraising, and staffing. 


  • A good deal of nonprofit-specific features

  • Great for growing nonprofits

  • Suitable for nonprofits with multiple locations

  • Advanced reporting capabilities

  • Automates administrative tasks

  • Grant tracking and billing

  • Fund accounting


  • Pricing is not publicly available 


  • Pricing depends on the size of your accounting team and the modules you choose to implement

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Go to Sage Intact’s official website


5. Xero (Top Nonprofit Financial Software for Growing Organizations)

xero accounting software

Why We Chose It:

Xero is similar to software like QuickBooks and Wave as it's not a dedicated financial software for nonprofits. Still, profit organizations also use it. The best part? It’s fully customizable to fit the needs of your growing nonprofit organization. 

Xero's strength lies in its extensive integration capabilities with over 1,000 third-party apps. This feature enables nonprofits to tailor the software to their specific needs.

For example, integrating Xero with tools like Infoodle allows for effective donation tracking, while the Gusto integration streamlines staff payroll processes. These integrations enhance Xero's functionality, making it a versatile tool that can handle various aspects of nonprofit financial management.

Additionally, you can generate all kinds of financial reports and even share those reports with board members, donors, and volunteers.


  • 30-day free trial

  • Great for growing nonprofit organizations

  • User-friendly and intuitive

  • 1000+ integrations

  • Comprehensive mobile app

  • 25% discount for nonprofits 


  • Payroll requires an additional fee

  • Lacks nonprofit-specific features


  • Early: $12/month

  • Growing: $34/month

  • Established: $65/month

Xero review

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Go to Xero’s official website


6. Zoho Books (Financial Management Software for Nonprofits on a Budget)

zoho books accounting software

Why We Chose It:

Zoho Books might not be a nonprofit-specific software, but it can easily be fine-tuned to meet the needs of your organization. The software is user-friendly and intuitive, so you can set it up and get started very quickly. 

You can contact the support team via phone, chat, or email if you hit a rough patch. Zoho Books is super useful if you have volunteers and other staff working from different locations. You can provide role-based access and let users work from any location online. 

You'll get an idea of your cash flow, your top expenses, and the projects that you undertake. You can even send payment receipts to your donors as a token of appreciation and proof of having received their contributions. 

One thing to note is that if you want to receive donations online in multiple currencies, you'll need to subscribe to Zoho Checkout, which will cost you $9 per month. 


  • 15% off for nonprofits 

  • Donations tracking

  • Comprehensive mobile app

  • Send payment receipts to donors

  • Monitor progress

  • Accept donations in multiple currencies

  • Free customer support 

  • Integrates well with other Zoho products


  • Requires separate subscription for receiving donations


  • Free

  • Standard: $15 /month billed annually 

  • Professional: $40 /month billed annually

  • Premium: $60 /month billed annually

  • Elite: $120 /month billed annually

  • Ultimate: $240 /month billed annually

Zoho Books review

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Go to Zoho Books’ official website


7. Blackbaud Financial Edge NXT (Good Nonprofit Treasurer Software for Large Organizations)

blackbaud financial edge nxt

Why We Chose It:

Blackbaud Financial Edge NXT is a great nonprofit treasurer accounting software for large nonprofits that want enterprise-level accounting. The software comes with advanced Financial Planning and Analysis tools, including budget predictions that will help you prioritize your expenses, assess your funding needs, and make comparisons across fiscal years. 

Large nonprofit organizations will be happy to hear the software offers grant accounting features. For instance, you’ll be able to track your grants by type, status, amount, and start/end dates with built-in fields and store grant-related information in one place. 

With Blackbaud Financial Edge NXT, you can manage your cash flow, accounts payable, and accounts receivable. On the plus side, it integrates with Blackbaud’s Raiser’s Edge, a capable tool for donor management and fundraising. 


  • Suitable for nonprofits with heavy accounting needs and a large donor base

  • Integrates seamlessly with Raiser’s Edge

  • Robust budgeting capabilities

  • Grant management 


  • Public pricing is unavailable 

  • Has a learning curve


  • The company doesn’t provide public pricing 

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Go to Blackbaud’s official website


8. Software 4 Nonprofits (Best Accounting Software for Small Nonprofits)

software 4 nonprofits

Why We Chose It:

Accounts by Software 4 Nonprofits is the best nonprofit software for small businesses with basic needs. 

The best thing about this software is that it's very affordable, costing only $95-$165 per year, and comes with all the basic features you would need to manage a small nonprofit such as tracking income and expenses. The software also lets you track funds. 

Another perk of this small nonprofit accounting software is that it's very easy to use, so you can onboard the system in a matter of a few hours. 

Keep in mind that all versions of the software work only on Microsoft Windows, except for the OnDemand version, which also works on Macs. Each version supports five organizations/databases. If you need features like donations tracking, you'll need to purchase a separate program called Donation, which will cost you an additional $30-$135 per year. 


  • 60-day trial period 

  • Very affordable

  • Supports five organizations/databases

  • On-demand version that works on Mac


  • The desktop program can only be used on Windows

  • You need to buy a separate program to track donors


  • Standard, $95 per year, includes email support and upgrades

  • OnDemand or Local Network, $165 per year, includes email support and upgrades

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Go to Software 4 Nonprofits’ official website


9. Money Minder (Great Nonprofit Bookkeeping Software for Volunteer-Led Organizations)

money minder

Why We Chose It:

MoneyMinder is a bookkeeping software for nonprofits built for volunteer-led organizations that need a simple and affordable solution. The software has two plans, Free and Pro. The Free plan comes with basic features, while the Pro plan unlocks more advanced features like volunteer management and bookkeeping tools. 

Volunteer management is where the software shines. You can easily track volunteer hours in relation to events, view reports by volunteers and events, evaluate events based on volunteer effort/time, and more. 

The software also lets you track donations, send donation acknowledgments, manage budgets, do bank reconciliation, and more. MoneyMinder comes with additional features that let you create an online store and access payments online, although these services come with additional fees. 


  • Free plan

  • Easy to use

  • Volunteer management tools

  • Donation tracking


  • Limited donor management tools

  • Bank integration requires additional fees


  • Free

  • Pro, $179/year  

Visit site
Go to Money Minders’ official website


10. FreshBooks (Best Fund Accounting Software for Nonprofit for Expense Tracking)

freshbooks dashboard

Why We Chose It:

In addition to being a very intuitive and user-friendly software, Freshbooks has a generous set of features and exceptional customer service. It lets you do everything from running reports, tracking expenses, and even tracking and logging time for your employees/volunteers. 

You can accept donations with secure online payments (such as via Paypal), set payment reminders, and activate recurring invoices. Other features include balance sheets, accounts receivable and payable, and general ledger tools. And if you want to send thank you emails to donors, you can create personalized thank you emails in a matter of seconds. 


  • Intuitive interface

  • All plans include time tracking and unlimited invoices 

  • 10% discount for an annual subscription

  • Supports all leading payment methods

  • Affordable 


  • Not suitable for nonprofits with complex operations  

  • All plans support one user

  • Adding additional users is expensive ($10/user/month)


  • Lite: $13.50 /month billed annually 

  • Plus: $22.50 /month billed annually 

  • Premium: $45 /month billed annually 

  • Select: contact vendor for pricing

Freshbooks review

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Go to Freshbooks’ official website


What is the Best Nonprofit Accounting Software for Me? Key Takeaways

Aplos is the best accounting software for nonprofits overall. It’s a fantastic tool if you’re looking for a solution that combines ease of use, affordability, and a generous set of features. 

However, this doesn’t mean this software would be a good fit for every nonprofit organization out there.

When choosing accounting software, consider the needs and financial capabilities of your organization. If you’re a smaller organization that works with a small group of volunteers, you’ll be better off with free or low-cost software that’s simple to use and offers basic accounting features—something like Wave or Accounts by Software 4 Nonprofits.

Additionally, take a look at this list of small business accounting software that lists 15 of the best options on the market today. 

If your nonprofit is larger, works with hundreds of donors, and accepts online payments, you’ll need a more robust solution—something like Xero or Sage Intacct. Large-scale nonprofits with more complex needs would be smart to go with advanced accounting software like QuickBooks Enterprise Nonprofit or Blackbaud. 

Almost every software solution on this list offers a free trial or demo tour. Take advantage of free trials/demos to test the software before you commit to a subscription or make a purchase. Check the prices of the monthly plans and see if you can afford them. If you’re planning to grow your business, you’ll need a platform that can grow with your business—so don’t forget to consider scalability.