The Best Accounting Software for Nonprofits and Small Businesses in 2025
Choosing the right accounting software is essential for keeping your nonprofit or small business finances in check. The right system will streamline bookkeeping, improve financial accuracy, and save you time. But with so many options available, which one should you choose?
We’ve ranked the top accounting software solutions based on ease of use, features, affordability, and suitability for nonprofits and small businesses. Let’s dive in!
1. QuickBooks Online – Best Overall
QuickBooks Online remains the gold standard for small businesses and nonprofits. It offers a full suite of accounting tools, user-friendly navigation, and seamless integrations.
Key Features:
✅ Cloud-based access from anywhere✅ Customizable reports for financial transparency✅ Automated invoicing and payment tracking✅ Integration with hundreds of business apps✅ Nonprofit-specific features like donor tracking and grant management
Why We Love It:
QuickBooks Online simplifies accounting with automation and powerful reporting tools. Whether you're managing daily expenses or preparing tax reports, QuickBooks makes it easy to stay compliant and organized.
2. Xero – Best for Growing Nonprofits & Businesses
Xero is a strong competitor to QuickBooks, offering robust accounting features with an intuitive interface.
Key Features:
✅ Unlimited users on all plans
✅ Bank reconciliation and expense tracking
✅ Customizable financial reporting
✅ Integrations with over 1,000 third-party apps
Why We Love It:
Xero is great for organizations that need collaboration across multiple users without extra costs. Its modern interface and automation tools make it an excellent choice for growing nonprofits and businesses.
3. FreshBooks – Best for Freelancers & Small Teams
FreshBooks is an excellent option for solopreneurs, consultants, and small nonprofit teams that need simple accounting tools without the complexity.
Key Features:
✅ Easy-to-use interface
✅ Time tracking and project-based accounting
✅ Automatic expense categorization
✅ Recurring invoices and payments
Why We Love It:
FreshBooks is user-friendly and built for professionals who need an accounting solution without a steep learning curve. It’s ideal for service-based businesses and nonprofits managing grants or donor funds.
4. Wave – Best Free Accounting Software
Wave is a top choice for small nonprofits and startups looking for a free accounting tool with essential features.
Key Features:
✅ 100% free accounting and invoicing
✅ Automatic expense tracking and bank syncing
✅ Customizable reports
✅ Payroll add-on available (paid)
Why We Love It:
Wave offers solid accounting features at no cost, making it a great option for cash-strapped nonprofits or startups just getting started.
5. Zoho Books – Best for Automation & Integration
Zoho Books is an affordable accounting software solution with strong automation and integration capabilities.
Key Features:
✅ AI-powered financial insights
✅ Automated workflows and approvals
✅ Multi-currency support
✅ Seamless integration with Zoho’s ecosystem
Why We Love It:
Zoho Books is great for organizations already using Zoho apps, offering a well-rounded accounting system with automation tools to save time.
Final Thoughts: Which One is Right for You?
For nonprofits and small businesses needing the best all-around accounting software: QuickBooks Online is the winner.
For growing organizations with multiple users: Xero is a fantastic choice.
For freelancers and small teams: FreshBooks is the easiest to use.
For those on a tight budget: Wave offers free accounting tools.
For automation lovers: Zoho Books is an integration powerhouse.
Still unsure? At Count 4 Causes, we help nonprofits and small businesses select and optimize their accounting software for financial success. Contact us today to find the best fit for your organization!