12 best accounting software for nonprofits In 2025

IYou know your way around a spreadsheet, but at some point, Excel alone isn’t enough to handle the unique financial needs of your growing nonprofit. Whether you're a finance manager, Executive Director, or board treasurer, the challenge isn’t about managing numbers—it’s about finding a tool that makes that job easier, more accurate, and more aligned with how your organization operates.

In this guide, we’ve rounded up 12 of the best accounting software for nonprofits—evaluated by price, features, nonprofit-specific functionality, and real user reviews—so you can confidently choose the right fit for your team, your reporting needs, and your mission.

12 best accounting software for nonprofits at a glance

We ranked these accounting platforms based on a combination of nonprofit-specific features, overall ease of use, affordability, scalability, and how well they integrate with fundraising tools like Givebutter. This list reflects the best overall fit for small to midsize nonprofits looking for practical, mission-aligned accounting solutions.

1. QuickBooks: Best overall for small to midsize nonprofits
2. Xero: Best for affordability and ease of use
3. FastFund: Best for grant tracking and nonprofit-specific reporting
4. Sage Intacct: Best for growing or enterprise-level organizations
5. Fund EZ: Best for user support and intuitive design
6. Aplos: Best for churches and faith-based organizations
7. Software4Nonprofits (Accounts): Best for offline fund accounting
8. MoneyMinder: Best for volunteer-run nonprofits and clubs
9. Wave Accounting: Best free accounting software 
10. Denali:  Best for security and audit controls
11. CustomBooks: Best for e-commerce fundraising
12. Blackbaud Financial Edge NXT: Best for large institutions with complex needs

1. QuickBooks: Best overall for small to midsize nonprofits

QuickBooks by Intuit offers reliable, scalable accounting software widely used by nonprofits. It’s become a go-to for many organizations thanks to strong reporting, flexible customization, and a growing ecosystem of nonprofit-friendly integrations—including a direct QuickBooks integration with Givebutter. Many teams can get up and running in under two hours, making it a solid choice for nonprofits that need trusted tools that work well together.

💰 Price: QuickBooks offers a 30-day free trial for new users. Standard plans range from $38/month (Simple Start) to $275/month (Advanced). Nonprofits can access discounted pricing through TechSoup

📣 Standout features: 

• Multiple payment processing methods, including credit card, bank transfer, and check
• Easy expense sorting
• Budget tracking
• AI accounting agents
• Customizable invoice templates
• Up to 40 users with custom permissions
• Specialized reports for nonprofits 

✅ Best for: Nonprofits that need an intuitive and reasonably priced option to manage their finances.

⭐ User satisfaction rating: 4.4/5

🔥 Our take: QuickBooks remains a go-to for many nonprofits thanks to its robust features, reliable reporting, and wide adoption in the sector. While rising subscription costs and limited functionality on lower-tier plans can be challenging for smaller organizations, discounts through TechSoup and strong integration options make it a smart, scalable choice for growing teams.

What users like about QuickBooks

It allows our charity to fully track our finances while integrating with a number of different software. These integrations allow us to track donations, pay contacts, and make purchases. — Bethany S., QuickBooks user

What users dislike about QuickBooks

What I don’t love about QuickBooks Online is that the reporting features—especially for financials and payroll—feel a bit limited. It would be great if we could filter reports by multiple fields at once, like department and project, without having to export everything to Excel. — Marsha J., Client Services Associate & QuickBooks user

Dive deeper

Save time with this nonprofit accounting cheat sheet →

2. Xero: Best for affordability and ease of use

Xero makes it easy to sync with your bank and other third-party apps—including an integration with Givebutter. Automated invoicing and reporting enable you to spend more time fundraising and less on bookkeeping. If you're a scaling organization, Xero also offers team-friendly tools that allow employees to submit expenses, send invoices, leave comments, and request time off.

💰 Price: ​​Plans start at $29/month. Xero offers a 25% discount for registered nonprofits, and all plans come with a 30-day free trial.

📣 Standout features: 

• Full mobile app for receipts, expenses, bills, and reconciliation  
• Tap to Pay on iPhone via Stripe, no hardware needed  
• Automated bill entry from mobile with draft conversion  
• Enhanced invoice features: keyboard shortcuts & drag‑drop attachments  
• Bank feeds & one-tap reconciliation with 21K+ banks

✅ Best for: Small nonprofits that want a clean, mobile-friendly accounting platform with essential features.

⭐ User satisfaction rating: 4.3/5

🔥 Our take: Xero is still loved for its simple, intuitive design, but recent price hikes and plan changes have made advanced features—like project tracking—available only on higher tiers. It’s a great starter tool, though some users are frustrated by the rising costs and gated functionality.

What users like about Xero

What I like best about Xero is its simplicity and smart design. Even if you're not from an accounting background, the interface is intuitive and easy to navigate. It doesn't overwhelm you with technical jargon or cluttered dashboards—everything is clean, straightforward, and just works. — Mustufa K., Assistant Manager of Finance and Accounts & Xero user

What users dislike about Xero

There is a learning curve for new users. Although the platform is user-friendly once you're familiar with it, some features—like tracking categories or setting up rules for bank reconciliation—can be slightly confusing at first without proper onboarding or tutorials. — Mustufa K., Assistant Manager of Finance and Accounts & Xero user

3. FastFund: Best for grant tracking and nonprofit-specific reporting

FastFund by Araize is a cloud-based accounting solution built specifically for nonprofits, with features like fund accounting, donation tracking, and integrated payroll. Designed to meet IRS and FASB compliance standards, it’s a strong option for organizations that need built-in tools for managing restricted funds and generating reports like Form 990. 

FastFund is accessible from any browser and continues to improve with updates like enhanced budgeting and customizable financial reports. 

💰 Price: Standard plan is $50/month. Premium plans run up to $94–$110/month depending on features, with payroll and fundraising modules available as add-ons for $20–$40/month each.

📣 Standout features: 

• FASB-compliant financial statements and IRS Form 990 generation
• Customizable reports and budget management
• Fund accounting and expense tracking
• Payroll and cash flow tools
• Cloud-based access (no mobile app)

✅ Best for: Small to mid-sized nonprofits needing affordable fund accounting with strong compliance support.

⭐ User satisfaction rating: 4.7/5

🔥 Our take: FastFund is a budget-friendly choice for compliance-focused nonprofits. It’s solid for managing accounting and tax requirements, but limited integrations and no mobile app may be a dealbreaker for tech-savvier teams.

What users like about FastFund

I know it sounds cliché, but this application is awesome. It is fast and so helpful in raising funds quickly for all kinds of fundraisers. — Casey C., Paralegal & FastFund user

What users dislike about FastFund

There is no alert or anything when you have pledge reminders that need to be generated, so you have to set a reminder elsewhere and then go into the system to take care of it. — Verified FastFund user

4. Sage Intacct: Best for growing or enterprise-level organizations

Sage Intacct is a cloud-based accounting platform built for complex nonprofit needs, offering powerful tools for fund tracking, grant management, revenue recognition, and customized reporting. It’s especially well-suited for mid-sized to large organizations that need robust functionality, including multi-entity support and integrations with tools like Givebutter and Salesforce. 

💰 Price: Custom quote required. Based on user reports, plans typically start around $3.5K to $9K per year, and can go as high as $50K to $70K for advanced features.

📣 Standout features: 

• Grant tracking and billing
• Real-time dashboards and reports
• AI-powered automation
• Revenue recognition
• Bulk billing updates

✅ Best for: Mid-to-large nonprofits that need advanced fund tracking, Salesforce integration, and robust reporting.

⭐ User satisfaction rating: 4.3/5

🔥 Our take: Sage Intacct is highly praised for its powerful nonprofit features and flexible integrations, especially with Salesforce. It’s a strong choice for growing organizations—but the high cost and steep learning curve can be a barrier for smaller teams.

What users like about Sage Intacct

Intacct provided a valuable solution to nonprofit accounting compared to the older financial systems that were being used. The cloud-based system allowed my team to work effectively at home without worrying about interruption, regardless of where you are. — Verified Sage Intacct user

What users dislike about Sage Intacct

It is very costly compared to other ERP software. It is also sometimes time-consuming. — Delina T., Accounting Specialist & Sage Intacct user

More to explore

Download your free nonprofit budget template →

5. Fund EZ: Best for user support and intuitive design

Fund EZ makes nonprofit accounting feel approachable with intuitive tools built specifically for mission-driven organizations. It handles everything from fund tracking and donor history to budgeting and reporting, all within a user-friendly interface and exceptional customer support. 

💰 Price: Custom pricing only; plan costs vary based on organization size and feature set. Free trial and demo available on request.

📣 Standout features: 

• Fund-based accounting for grants, programs, and departments
• Automated financial report generation
• Donor and pledge tracking with matching gift tools
• Bank reconciliation and accounts payable management
• Budgeting with real-time dashboard views

✅ Best for: Medium to large nonprofits that need guided support and nonprofit-specific features.

⭐ User satisfaction rating: 4.5/5

🔥 Our take: Fund EZ remains a solid option for nonprofits prioritizing ease of use and support. It’s particularly helpful for orgs that want guided setup and transparent nonprofit reporting, though it may feel limited for teams that need advanced customization or integrations.

What users like about Fund EZ

Fund EZ is an awesome tool for budget management for nonprofit projects. It helps with forecasting, accounts payable and receivable, billing and invoicing, general ledger management, and financial reporting. — Andrew G., Manager & Fund EZ user

What users dislike about Fund EZ

Great software, but it would be great if it worked on Mac desktop, mobile, iPad, and also if it had a trial version so anyone can try before the actual purchase. Apart from this, it’s an awesome app. — Amit Y., Freelance Professional & Fund EZ user

6. Aplos: Best for churches and faith-based organizations

Aplos is an all-in-one cloud-based platform designed for nonprofits and churches that need more than basic bookkeeping. It combines fund accounting with donation tracking, budgeting, payroll, and event management—making it especially useful for faith-based organizations managing multiple funds, ministries, or campaigns.

💰 Price: Standard plans start at $79/month for the Lite/basic tier, with higher-tier plans available at increased rates. Short-term promotional discounts and special bundle deals are sometimes offered for churches and small nonprofits.

📣 Standout features: 

• Fund and church-specific accounting
• Donor CRM and giving reports
• Dimensional budgeting and ministry reporting
• Data visualizer and dashboards
• Integrated payroll and event tracking
• Online donations and text-to-give

✅ Best for: Churches or ministries that need purpose-built software to manage giving, accounting, and member engagement.

⭐ User satisfaction rating: 4.7/5

🔥 Our take: Aplos remains a top pick for faith-based nonprofits thanks to its simplicity and church-specific tools. However, price increases after the first year and limited reporting flexibility may be a concern for growing teams. Plus, some users on G2 note slow customer service response times and a lack of customization in reporting.

What users like about Aplos

We switched from QuickBooks to Aplos nearly three years ago, and we've never regretted the switch for one second. Aplos is genuinely a financial software package for nonprofits. It fits our needs well. Using software designed specifically for a nonprofit makes a world of difference. — Kevin L., Finance Director & Aplos user

What users dislike about Aplos

I would like to be able to report on two levels of tags. For example, by department AND project. I would like to have an option in the drop-down list for report date range to be YTD through last month because each month when I do custom reports, I have to plug in the dates manually, and it’s time-consuming. — Kassie B., Finance Manager & Aplos user

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7. Software4Nonprofits (Accounts): Best for offline fund accounting

Accounts by Software4Nonprofits is a desktop-based accounting tool built for nonprofits that prefer a simple, offline solution. It delivers double-entry bookkeeping, customizable nonprofit reports, and clear fund tracking—all without the clutter of features you don’t need. With optional integration to their donation tracking tool, Donations, it's a smart, low-cost pick for small teams, rural orgs, or anyone working without reliable internet.

💰 Price: Plans range from $129-$199/year. The optional Donations module is priced by donor volume, starting at $17/month for 100 donors.

📣 Standout features:

• Fund accounting with classes and categories
• Customizable reports and statements
• Import/export with Excel and QuickBooks
• Audit-friendly documentation
• Optional integration with their donation tracking software (Donations)

✅ Best for: Smaller to mid-sized nonprofits that want a low-cost, offline solution.

⭐ User satisfaction rating: 5/5

🔥 Our take: Accounts is a mobile-optimized donation app, which makes it a plus for nonprofits. It's a solid option for nonprofits that prefer desktop-based systems or work in low-connectivity areas.

What users like about Accounts

Accounts is very easy to navigate and helps me run my business smoothly. It’s easy to enter information for processing and keep track of all the budgeting. — Ania Z., Managing Director & Accounts user

What users dislike about Accounts

Accounts has no faults for me except the pricing maybe. — Ania Z., Managing Director & Accounts user

8. MoneyMinder: Best for volunteer-run nonprofits and clubs

MoneyMinder is a simple, cloud-based accounting tool built for volunteer-led organizations, clubs, and community groups. It’s designed for ease and transparency, with just the right features for teams that don’t have a dedicated finance expert. With flat-rate pricing, a no-fuss interface, and tools made specifically for treasurers, it’s a reliable choice for small organizations that want to stay organized without overcomplicating things.

💰 Price: $299/year (flat rate for all users), with a free version available.

📣 Standout features:

• Treasurer-specific dashboard
• Donation and dues tracking
• Budget-to-actual reporting
• Volunteer roster and calendar
• Year-end financial summary generator

✅ Best for: Volunteer-led nonprofits or clubs that need transparency and simplicity.

⭐ User satisfaction rating: 4.6/5

🔥 Our take: If mostly volunteers run your nonprofit or leadership rotates often, MoneyMinder’s user-friendly platform is a strong fit. That said, it's not ideal for organizations that need advanced reporting or payroll capabilities.

What users like about MoneyMinder

It is the best accounting tool we have used. It is also very secure and reliable because it automatically backs up your full account every 24 hours. I love the integration with G Suite to import sheets and calculations, print, and other options. In addition, [MoneyMinder] allows us to manage volunteers, donors, and members of our association, so it is vitally important when generating reports. — Yaxis M., MoneyMinder user

What users dislike about MoneyMinder

There is no way to revert to previous budgets, so if you decide to do a budget revamp and it doesn't pass at your meeting, you will need to retype the entire thing. I am sure it is pretty easy to add a feature to edit. — Utsav N., KDP Consultant & MoneyMinder user

9. Wave Accounting: Best free accounting software 

Wave is a free accounting software for small nonprofits with simple bookkeeping needs. While it’s not built specifically for nonprofits, it offers essential tools like income and expense tracking, invoicing, and basic reporting—all at no cost. For lean teams or newer organizations just getting started, Wave is an easy way to stay organized without stretching your budget.

💰 Price: Core accounting tools are free, with the Pro plan priced at $16/month. Paid add-ons are available for payroll features and bookkeeping services. 

 📣 Standout features:

• Unlimited income and expense tracking
• Invoice and payment tools
• Simple financial reporting
• Bank connection and reconciliation
• Free email support

✅ Best for: Small nonprofits with limited budgets and minimal accounting needs.

⭐ User satisfaction rating: 4.3/5

🔥 Our take: Wave offers exceptional value—especially for organizations that don’t need complex fund tracking or integrations. However, the free plan does not include nonprofit-specific features like donor tracking or fund restriction reporting.

What users like about Wave Accounting

The free version is great for a startup nonprofit. It is easy to navigate for someone without a finance background. Customer support has always been helpful. — Verified Wave user

What users dislike about Wave Accounting 

 The amount of integrations available is lacking. — Verified Wave user

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10. Denali: Best for security and audit controls

Denali, by Cougar Mountain Software, is a nonprofit accounting solution focused on fraud prevention, compliance, and data security. While it isn’t as feature-rich as some competitors, it offers strong internal controls and secure access—making it a reliable choice for organizations that handle sensitive financial data.

💰 Price: Custom quote required. Pricing varies by module and user count, but expect $999+ for basic configurations and annual maintenance fees.

📣 Standout features: 

• Fraud prevention and internal controls
• Compliant nonprofit accounting
• Customizable financial reports
• Access to donor management tools
• Audit-ready fund tracking

✅ Best for: Nonprofits that prioritize data security and financial compliance.

⭐ User satisfaction rating: 3.9/5

🔥 Our take: Denali delivers on security and fraud protection, which makes it a strong fit for cautious or compliance-driven nonprofits. However, its limited feature depth and technical complexity may require additional training for smaller or less tech-savvy teams.

What users like about Denali Business

Our organization has federal grants, private grants, corporate sponsorships, etc., all with different reporting requirements and budgets. We also have seven locations, and Denali is able to track by the funding sources and locations. — John C., Manager & Denali Business user

What users dislike about Denali Business

For the features they offer, they are pretty expensive. Other substitutes are available. — Audrey B., Sales Manager & Denali Business user

11. CustomBooks: Best for e-commerce fundraising

CustomBooks (previously AccountingSuite) is a cloud-based accounting and inventory platform originally built for small businesses. While its core audience is still small teams, the platform is flexible enough for nonprofits managing product sales, event merch, or project-based budgets. It combines bookkeeping, order management, inventory, and time tracking in one centralized system.

💰 Price: Free trial available (no credit card required!). Plans start at $19/month for the entry-level StartUp tier. Higher-tier plans, priced at $55/month and up, add features like advanced inventory management, expanded user seats, and enhanced reporting. 

📣 Standout features: 

• Intuitive dashboard
• Mobile app access
• Project and time tracking
• Customizable financial reports
• Inventory and order management
• Purchase and sales tracking
• Bank reconciliation

✅ Best for: Small nonprofits that use e-commerce as a fundraising technique and need one central place to house all of their finances.

⭐ User satisfaction rating: 4.4/5

🔥 Our take: CustomBooks offers an affordable plan for nonprofits that don’t require many users, making it perfect for small organizations that need a simple, centralized solution. However, because the platform wasn’t built with nonprofits in mind, it lacks some crucial features and integrations.

What users like about CustomBooks

What I like best about CustomBooks is how it combines dual-entry accounting with inventory management in one platform. It’s intuitive, affordable, and gives me clear, accurate financial insights without needing extra tools or plugins. — Verified CustomBooks user

What users dislike about CustomBooks

For some, it may be expensive and complex to use because its features are advanced. —  Shubhanghi B., Marketing Associate & CustomBooks user

12. Blackbaud Financial Edge NXT: Best for large institutions with complex needs

Blackbaud Financial Edge NXT is a powerful, cloud-based accounting platform built for large nonprofits with complex funding streams and reporting needs. It’s a strong fit for institutions that require advanced grant tracking, multi-fund accounting, and in-depth financial analysis—especially if they’re already using other tools in the Blackbaud ecosystem to manage donors, programs, or operations.

💰 Price: Premium-priced, by custom quote, generally significantly higher than entry-level tools—cost is typically tailored for large organizations.

📣 Standout features:

• End-to-end fund accounting
• Role-based dashboards
• Audit-ready reports
• Seamless integration with Raiser’s Edge NXT
• FASB and IRS compliance tools

✅ Best for: Larger nonprofits managing multiple programs or grants and needing enterprise-level accounting controls.

⭐ User satisfaction rating: 4.0/5

🔥 Our take: Financial Edge NXT is a worthy consideration if your nonprofit is scaling quickly or managing a large number of restricted funds and programs. The platform was built specifically for nonprofits, and it shows. However, it may be overkill (and too expensive) for smaller orgs with basic needs.

What users like about Blackbaud Financial Edge NXT

NXT is user-friendly and offers an array of features. They provide a number of webinars and trainings on any new features or transitions, which makes the implementation easier. — Becky L., Accounts Payable Supervisor & Blackbaud Financial Edge NXT user

What users dislike about Blackbaud Financial Edge NXT

Overall, the product is expensive, especially for a nonprofit. You pay for what you get. Premium price for a high-quality product. —  Verified Blackbaud Financial Edge NXT user

More to explore

Find the right funding mix for your nonprofit →

What to look for in nonprofit accounting software 

Whether you're choosing your first accounting tool or upgrading to a more powerful solution, it's important to find accounting software for your nonprofit organization that balances usability, affordability, and compliance—especially if you're a new team looking for small nonprofit accounting software that won’t overcomplicate your workflow.

• Financial reporting 📈 The software should offer customizable financial statements and custom report generation.
  
• Integrations ⚒️ Consider whether the accounting software integrates with other systems like a CRM or fundraising platform.
  
• Ease of use 💻 Look for a tool that’s accessible to users with different skill levels so your entire team can contribute to the financial process.
  
• Compliance and regulation support ✅ Ensure that the platform can generate the necessary reports for audits and regulatory filings.
  
• Security and data protection 🚫 Look for robust security features like user access controls and regular data backups.
  
• Cost and affordability 💰 Check subscription fees, implementation costs, and any additional charges for support or training.
  
• Nonprofit-specific features 💛 Some platforms are specifically designed for nonprofit organizations and offer tools like donation tracking and membership management.

Supercharge your nonprofit’s financial management with Givebutter 

With so many accounting tools, the right pick comes down to your team’s needs, reporting requirements, and how well it fits into your existing systems. Use this guide to compare your options, check in with your finance team, and find the best fit for your organization.

No matter which platform you choose, pairing it with a fundraising system like Givebutter ensures your data stays clean, organized, and easy to reconcile. Givebutter’s integrations with QuickBooks, Xero, Sage Intacct, and other tools help your fundraising and finance tools work better together—so you can spend less time exporting spreadsheets and more time moving your mission forward.

👉 Create your free Givebutter account today to see how easy it is to plug into your financial flow.

FAQs about accounting software for nonprofit organizations

How much should a nonprofit spend on accounting software?

Most nonprofits spend $0–$200/month, depending on their size and specific needs. Costs vary based on features like fund tracking, user seats, and integrations. Free tools like Wave can work well for smaller organizations, while larger ones may need paid platforms like Blackbaud or Sage Intacct.

Should small nonprofits invest in specialized accounting software?

Yes—especially if you're managing donations, grants, or restricted funds. Specialized nonprofit accounting software offers features like fund tracking and donor reporting that general business tools typically lack.

How do I transition from spreadsheets to accounting software?

Start by cleaning up your spreadsheet data—remove duplicates, fix formatting, and organize categories. Then map your budgets, expenses, and income into your new tool’s structure. Most platforms offer import templates or onboarding support to simplify the switch.

Can I use multiple accounting platforms together?

It's possible, but not ideal. Using multiple accounting platforms can lead to errors or data inconsistencies. Instead, look for tools that integrate with your CRM, donation platform, or payroll system so everything stays in sync.

How long does it take to implement new accounting software?

Setup can take anywhere from a few hours to several weeks. Simple tools like Wave or QuickBooks can be up and running in a day, while more complex platforms like Sage Intacct may require staff training and data migration planning.