With the right accounting tools, you can accurately track funding sources, ensure compliance with financial regulations, and make smarter decisions about resource allocation.
However, not all accounting software is built with nonprofits in mind. Some offer essential budgeting and reporting tools, while others provide specialized nonprofit features like fund accounting, grant tracking, and donor management.
To help you make the right choice, we’ve rounded up 13 of the best accounting software for nonprofit organizations in 2025.
Whether you’re a small nonprofit looking for a cost-effective solution or a larger organization needing advanced automation and reporting, there’s an option for you.
Nonprofits have unique financial management needs, which is why we carefully evaluated each option based on the features that matter most to them.
Here’s what we considered when choosing the best accounting software for nonprofit organizations:
To kick off our list of the best accounting software for nonprofit organizations, we’ll highlight those that offer industry-specific features.
These tools make fund accounting easier, improve financial transparency, and ensure compliance with nonprofit regulations.
Image via Aplos
Aplos is a top choice for accounting software for nonprofit organizations, especially faith-based organizations. It’s designed to simplify fund accounting, making it easy to track donations, grants, and expenses while maintaining transparency.
With features like fund-based balance sheets and income statements, this nonprofit accounting software helps you stay accountable and monitor your nonprofit’s financial health.
You can also create reports and compare the budget of your nonprofit to actual spending across different funds or tags, giving you a clear picture of where your money is going.
Beyond accounting, Aplos offers tools to help you boost donations, including online donation forms and a Text to Give feature.
Besides, its built-in CRM database lets you create donor profiles, segment your donor list, and personalize communication to strengthen donor relationships.
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Aplos provides a 15-day free trial and three paid plans:
Image via Aplos
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Image via AccuFund
AccuFund is a robust accounting solution designed for large nonprofits and government organizations that need powerful financial management tools. Whether you prefer an on-premise or cloud-based system, nonprofit accounting software offers flexibility to fit your organization’s needs.
With features like fund accounting, in-depth reporting, a customizable dashboard, and automation tools, AccuFund simplifies complex financial tasks, saving your team time and effort.
This accounting software for nonprofit organizations provides a full suite of nonprofit-specific tools, including:
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Image via Blackbaud
Blackbaud Financial Edge NXT is a robust fund accounting software for nonprofit organizations. It simplifies financial management by automating routine tasks and creating intuitive workflows, saving you time and effort.
What makes Blackbaud stand out is its ability to tackle common financial challenges while improving transparency.
With flexible reporting, you can track financial data by project, grant, or any custom category that fits your needs. Plus, budgeting tools help you manage restricted funds with ease.
When the need arises, you can show your stakeholders the financial activities associated with each fund and grant without running a report.
The nonprofit accounting software also integrates seamlessly with other Blackbaud tools like Raiser’s Edge NXT.
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Just like AccuFund, Blackbaud doesn’t display the pricing information on its website. You have to contact the sales team for pricing information.
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Image via QuickBooks
Quickbooks is another top accounting software for nonprofit organizations, offering a range of features designed to streamline financial management, including cloud-based accounting tools.
While the core QuickBooks platform is great, QuickBooks Enterprise for Nonprofits goes a step further with tools tailored specifically to nonprofit budget needs.
Along with standard accounting features, you’ll get:
This nonprofit accounting software system is one of the top choices because it also integrates with other essential tools, like payroll software, making it a comprehensive solution.
While QuickBooks Enterprise is a desktop-based software, a cloud-access version is also available for added flexibility.
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With QuickBooks, you can choose either to get a 30-day free trial or a 50% off discount for 3 months if you buy right away. The paid plans are:
Image via QuickBooks
There are also Enterprise plans available, with the following starting prices:
Image via QuickBooks
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Image via Araize
FastFund by Araize is a powerful accounting software for nonprofit organizations, designed by experts who understand nonprofit accounting.
With FastFund, you can:
What makes it one of the best accounting software for nonprofits is that you get the option to integrate fundraising and payroll services into the system.
The premium plan includes accounts payable, accounts receivable, and direct cost allocations. Indirect cost allocations and purchase orders are available as an add-on.
Users also get expert training in nonprofit accounting and bookkeeping. This ensures that you’re always equipped to manage your organization’s finances with confidence.
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FastFund provides a fully functional online trial version with a demo data set and two paid plans. Add-ons are also available, each at a certain monthly cost. Check out the pricing for the paid plans below:
Image via Araize
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Image via MoneyMinder
MoneyMinder is the right accounting software for nonprofit organizations that can’t afford to hire accounting experts.
Designed with volunteers in mind, it simplifies bookkeeping by cutting out the confusing nonprofit accounting jargon and complex processes.
You can easily create a chart of accounts tailored to your organization’s activities, track budgets, and generate financial forecasts.
The MoneyMinder Store feature also makes it easy to sell merchandise, event tickets, and more. Plus, you can collect online payments, membership dues, and donations through Stripe, PayPal, and other payment options.
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Image via MoneyMinder
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Image via NetSuite
NetSuite is a cloud-based ERP designed to handle everything from accounting and financial management to CRM and human capital management.
For nonprofits, it offers a comprehensive suite of cloud-based accounting software, including fund management, grant accounting, and spend tracking. It helps organizations streamline operations and stay on top of their finances.
With automation features, you can simplify transactions, ensure compliance, and close your books with ease. Real-time reporting also gives donors and stakeholders full transparency into your organization’s financial health.
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Image via Fund EZ
Fund EZ is a great accounting software for nonprofit organizations that features a flexible multi-segment chart of accounts, giving you a clear view of your programs, projects, and funding streams.
To help you track progress from different angles, the platform offers unlimited dashboards with intuitive grids, pie charts, and bar graphs.
If you need custom reports for donors or board members, you can generate tailored reports and even apply allocation as needed.
This nonprofit accounting software lets you set up multiple cost centers. You can bill clients and allocate the revenue across your chart of accounts.
You can also enhance its capabilities with optional add-ons like fixed asset accounting and a fundraising platform.
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Image via NonProfit+
NonProfit+ is one of the best all-in-one accounting software solutions designed specifically for nonprofit organizations.
Beyond fund accounting, it offers essential tools for:
The NonProfit+ accounting suite makes it easy to prevent the commingling of funds.
You can get additional features through the financial management suite. This includes accounts receivable and payables, currency management for global nonprofit organizations, and automated billing.
A procurement management suite is also available as an add-on.
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Image via MIP Fund Accounting
MIP Fund Accounting is another top cloud-based, SaaS fund accounting software for nonprofit organizations. Its scalability makes it a great choice for nonprofits that need a solution that grows with them. You can start with the modules you need and add more as your nonprofit expands.
With MIP Fund Accounting, you can generate detailed financial reports based on funding sources, programs, and locations. Its customizable chart of accounts lets you easily track grants, funds, projects, and more.
The accounting software for nonprofit organizations also allows you to create budgets for specific grants and across multiple periods. A standout feature that sets it apart is its ability to track volunteer hours, alongside managing inventory, fundraising, and even employee records.
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The following accounting software cut across industry boundaries, but are still effective in streamlining the financial operations of nonprofit organizations.
They provide robust functionalities for fund and expense tracking, basic accounting tasks, compliance management, online donations, transparent reporting, and more.
Image via Xero
Xero is a great online accounting software for all businesses, nonprofits included. Its advanced analytics give you a clear view of the financial health of your nonprofit, helping you track key metrics, forecast short-term cash flow, and compare actual reports with different financial scenarios.
What sets Xero apart is its highly customizable reporting, featuring an intuitive drag-and-drop interface that makes it easy to tailor financial insights to your needs.
While there are many other Xero alternatives, few offer this level of flexibility and depth in financial reporting.
Beyond accounting, Xero simplifies payroll management and record-keeping. With integrations for over 20 of some of the best CRMs, reporting tools, and expenses apps, you can easily connect it with your existing systems for a more streamlined workflow.
Some popular integrations include Keela, MembershipWorks, and Hubdoc.
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This accounting software for nonprofit organizations offers a 30-day free trial and three paid plans:
Image via Xero
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Image via Intacct
Sage Intacct is a cloud accounting tool for all types of businesses, including nonprofit organizations with a global presence.
With built-in support for multi-currency transactions and tax filing across different jurisdictions, it simplifies financial management for organizations with an international reach.
One of the key benefits of Sage Intacct is its powerful AI-driven automation. With just one click, you can consolidate accounts, generate real-time performance insights, and streamline your financial reporting.
Its robust nonprofit accounting features allow you to create detailed statements based on revenue sources. You can also customize accounts for each funder and more.
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Image via FreshBooks
FreshBooks is a comprehensive accounting software for nonprofit organizations. With a customizable chart of accounts, you can tailor it to fit your nonprofit’s unique needs — whether that’s to track restricted funds, grants, donations, or program expenses.
One of the best capabilities of this financial accounting software is the ability to manage time tracking and invoicing in one platform. Time tracking enables you to use your volunteers’ time efficiently.
FreshBooks Payments makes it easy to accept donations and payments via credit cards, ACH, and checkout links. You can also keep track of expenses and keep your tax records ready for tax season.
Besides, with automated notifications for invoices and payment receipts, you can keep donors and stakeholders in the loop with ease.
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The accounting software for nonprofit organizations offers a 30-day free trial and four paid plans:
Image via FreshBooks
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With so many great accounting software for nonprofit organizations, finding the right accounting software can feel overwhelming. To help you make the best choice, here are four key factors to consider:
While cost is an important factor when choosing the best accounting software for nonprofit organizations, it’s essential to look beyond the initial price.
Many nonprofit accounting tools offer different pricing models, including subscription-based plans or one-time purchases. When choosing an accounting software, pay close attention to additional fees, such as setup costs, transaction fees, or charges for extra users.
Here’s what to consider:
Not all accounting software is built for nonprofits. Some tools cater primarily to businesses and may lack essential nonprofit-specific functionalities.
Therefore, before making a decision, outline your organization’s financial management needs. Here are some features to look out for:
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Your nonprofit might be small now, but as you expand, your financial management needs will grow. The last thing you want is software that becomes a limitation instead of a solution.
So opt for scalable accounting software for nonprofit organizations that:
The selected accounting software for nonprofit organizations shouldn’t work in isolation, it needs to integrate with the other tools your nonprofit relies on.
Before choosing an accounting platform, check if it connects smoothly with your payroll system, donor management software, fundraising tools, and grant tracking systems.
The key integrations to look out for include:
1. What is nonprofit accounting software and how is it different from regular accounting software?
Nonprofit accounting software is a specialized financial management tool designed specifically for charities, foundations, churches, and other nonprofit organizations.
It uses fund accounting to track multiple revenue streams separately, distinguishing between restricted and unrestricted funds. This ensures accurate fund management and compliance with donor restrictions and financial regulations.
In contrast, regular accounting software focuses on tracking income, expenses, and profitability for businesses aiming to maximize profits without the need to manage funds based on donor-imposed limitations.
2. Do nonprofits need fund accounting software?
Yes, fund accounting software is crucial for nonprofits because it ensures that donor-restricted and unrestricted funds are properly tracked and used for their intended purposes.
It also simplifies reporting to stakeholders, grant providers, and tax authorities. Many nonprofit accounting software solutions offer built-in fund accounting features.
3. Is there free accounting software for nonprofit organizations?
Yes, there are free accounting software options that cater to nonprofit organizations, offering essential financial management tools without the hefty price tag.
A great example of accounting software for nonprofit organizations that offer a free plan is MoneyMinder.
The platform’s free version has limited yet essential features, including:
4. Is there a QuickBooks version for nonprofit organizations?
Yes, QuickBooks offers one of the best accounting software for nonprofit organizations. It’s known as the QuickBooks Enterprise nonprofit software. It’s available as a desktop program, but you can also opt for cloud access.
5. What is the best accounting method for nonprofit organizations?
The accrual accounting method is the best approach, as it ensures compliance with GAAP. However, since it’s a complex method, it’s more appropriate for large nonprofit organizations.
On the other hand, the cash accounting method is the most suitable for small nonprofit organizations due to its simplicity.
6. What accounting is used for nonprofit organizations?
Nonprofit organizations use fund accounting. It employs a unique approach to tracking donations and expenses. Money from various sources, such as donations, membership fees, and grants, is accounted for separately. Each source has its own set of accounts and financial statements.
7. What is the best accounting software for a small charity?
Some of the best nonprofit accounting software for small charities include:
8. Can accounting software help nonprofits with tax compliance?
Yes, many accounting software for nonprofit organizations include automated tax reporting, Form 990 preparation, and compliance tracking to ensure organizations follow IRS and state regulations. These tools help nonprofits maintain tax-exempt status and simplify financial audits.
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Now that we’ve listed 13 of the best accounting software for nonprofit organizations, you should have a good idea of which one works best for you.
However, we simply can’t decide the perfect accounting software for your nonprofit organization. Your choice will depend on your budget, unique organizational needs, and scalability requirements.
What we’d recommend is that you compare each of the listed software’s features, pros, and cons. Pick a handful of tools that you think would be a good fit for your organization. Then, sign up for their free trials to make an informed decision on which one best fits the criteria you’re looking for.
For more in-depth resources on nonprofit accounting, bookkeeping best practices, and expert tips, check out our accounting resource hub. It’s packed with guides and tools to help your organization manage its finances more effectively.
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