Quick Overview
- 1#1: Aplos - Cloud-based accounting software designed specifically for small nonprofits, featuring fund accounting, donation tracking, and Form 990 support.
- 2#2: QuickBooks Online - Versatile cloud accounting platform with nonprofit edition, class tracking for funds, and extensive integrations for small organizations.
- 3#3: Xero - User-friendly cloud accounting for small nonprofits with bank feeds, multi-currency support, and customizable reporting.
- 4#4: Wave - Free accounting software offering invoicing, expense tracking, and basic reporting ideal for very small nonprofits.
- 5#5: ZipBooks - Free starter accounting tool with invoicing, time tracking, and financial reports suitable for small nonprofit operations.
- 6#6: Zoho Books - Affordable online accounting with project tracking, multi-location support, and automation for growing small nonprofits.
- 7#7: FreshBooks - Intuitive invoicing and light accounting software with expense management and client portals for small nonprofit teams.
- 8#8: Odoo - Open-source ERP platform with modular accounting, inventory, and nonprofit apps for customizable small organization finance.
- 9#9: Manager - Free open-source desktop and cloud accounting software supporting double-entry bookkeeping and custom reports for nonprofits.
- 10#10: GnuCash - Free open-source accounting program with double-entry and multi-account fund tracking for personal and small nonprofit use.
We ranked tools by their focus on core nonprofit requirements (fund accounting, donation tracking, compliance readiness), usability for small teams, technical reliability, and value, ensuring the list includes both affordable and feature-rich options that cater to various budgets and operational scales.
Comparison Table
This comparison table simplifies choosing accounting software for small nonprofits by examining tools like Aplos, QuickBooks Online, Xero, Wave, ZipBooks, and more, guiding users through key features and suitability. Readers will discover how each platform balances functionality—from donor tracking to reporting—and aligns with varying needs, enabling informed decisions for their organization.
| # | Tool | Category | Overall | Features | Ease of Use | Value |
|---|---|---|---|---|---|---|
| 1 | Aplos Cloud-based accounting software designed specifically for small nonprofits, featuring fund accounting, donation tracking, and Form 990 support. | specialized | 9.6/10 | 9.8/10 | 9.4/10 | 9.3/10 |
| 2 | QuickBooks Online Versatile cloud accounting platform with nonprofit edition, class tracking for funds, and extensive integrations for small organizations. | enterprise | 8.5/10 | 8.0/10 | 9.2/10 | 8.3/10 |
| 3 | Xero User-friendly cloud accounting for small nonprofits with bank feeds, multi-currency support, and customizable reporting. | specialized | 8.2/10 | 7.9/10 | 9.1/10 | 8.0/10 |
| 4 | Wave Free accounting software offering invoicing, expense tracking, and basic reporting ideal for very small nonprofits. | other | 7.6/10 | 6.2/10 | 9.4/10 | 9.7/10 |
| 5 | ZipBooks Free starter accounting tool with invoicing, time tracking, and financial reports suitable for small nonprofit operations. | other | 7.2/10 | 6.4/10 | 8.7/10 | 8.9/10 |
| 6 | Zoho Books Affordable online accounting with project tracking, multi-location support, and automation for growing small nonprofits. | specialized | 8.1/10 | 7.8/10 | 9.2/10 | 9.4/10 |
| 7 | FreshBooks Intuitive invoicing and light accounting software with expense management and client portals for small nonprofit teams. | other | 6.8/10 | 5.2/10 | 9.2/10 | 7.1/10 |
| 8 | Odoo Open-source ERP platform with modular accounting, inventory, and nonprofit apps for customizable small organization finance. | enterprise | 7.6/10 | 8.1/10 | 6.4/10 | 8.7/10 |
| 9 | Manager Free open-source desktop and cloud accounting software supporting double-entry bookkeeping and custom reports for nonprofits. | other | 7.2/10 | 6.8/10 | 8.7/10 | 9.5/10 |
| 10 | GnuCash Free open-source accounting program with double-entry and multi-account fund tracking for personal and small nonprofit use. | other | 7.2/10 | 7.0/10 | 5.8/10 | 9.5/10 |
Cloud-based accounting software designed specifically for small nonprofits, featuring fund accounting, donation tracking, and Form 990 support.
Versatile cloud accounting platform with nonprofit edition, class tracking for funds, and extensive integrations for small organizations.
User-friendly cloud accounting for small nonprofits with bank feeds, multi-currency support, and customizable reporting.
Free accounting software offering invoicing, expense tracking, and basic reporting ideal for very small nonprofits.
Free starter accounting tool with invoicing, time tracking, and financial reports suitable for small nonprofit operations.
Affordable online accounting with project tracking, multi-location support, and automation for growing small nonprofits.
Intuitive invoicing and light accounting software with expense management and client portals for small nonprofit teams.
Open-source ERP platform with modular accounting, inventory, and nonprofit apps for customizable small organization finance.
Free open-source desktop and cloud accounting software supporting double-entry bookkeeping and custom reports for nonprofits.
Free open-source accounting program with double-entry and multi-account fund tracking for personal and small nonprofit use.
Aplos
specializedCloud-based accounting software designed specifically for small nonprofits, featuring fund accounting, donation tracking, and Form 990 support.
True multi-fund accounting that automatically allocates transactions across restricted and unrestricted funds in real-time
Aplos is a cloud-based accounting software tailored specifically for small nonprofits, churches, and ministries, providing fund accounting to track restricted and unrestricted funds seamlessly. It integrates donor management, budgeting, payroll, and automated reporting for Form 990 preparation and grant compliance. With its intuitive interface, Aplos simplifies complex nonprofit financial tasks while ensuring accuracy and regulatory adherence.
Pros
- Specialized fund accounting handles multi-fund tracking effortlessly
- Integrated donor database and online giving tools streamline fundraising
- Robust reporting and 990 e-filing save time on compliance
Cons
- Limited advanced inventory management for orgs with product sales
- Payroll add-on increases costs for smaller budgets
- Customer support primarily business hours, no 24/7 live chat
Best For
Small nonprofits, churches, and ministries seeking affordable, nonprofit-specific accounting without the complexity of enterprise solutions.
Pricing
Starts at $59/month (Basic), $99/month (Growth), $159/month (Pro), plus add-ons like payroll ($45+/mo); free trial available.
QuickBooks Online
enterpriseVersatile cloud accounting platform with nonprofit edition, class tracking for funds, and extensive integrations for small organizations.
Class and location tracking enabling seamless multi-fund accounting without complex setup
QuickBooks Online is a cloud-based accounting software from Intuit, widely used by small businesses and nonprofits for managing finances, invoicing, expense tracking, and bank reconciliations. For small nonprofits, it supports fund accounting through class and location tracking, donor management via customer records, and customizable reports for grants and donations. It integrates with apps like Donorbox or Classy to handle specialized nonprofit needs like pledge tracking and event registration.
Pros
- Intuitive interface with strong mobile app support
- Excellent bank feeds and automation for reconciliations
- Vast app marketplace for nonprofit integrations
Cons
- Nonprofit-specific features like grant tracking require workarounds or add-ons
- Higher-tier plans needed for advanced reporting can increase costs
- Limited built-in donor relationship management compared to dedicated tools
Best For
Small nonprofits with basic to moderate accounting needs that value ease of use and scalability over deep specialized nonprofit functionality.
Pricing
Starts at $30/month (Simple Start) to $200/month (Advanced); nonprofits eligible for 30-50% discounts and 90-day free trials.
Xero
specializedUser-friendly cloud accounting for small nonprofits with bank feeds, multi-currency support, and customizable reporting.
Unlimited users across all plans, enabling easy collaboration for small nonprofit teams without extra costs
Xero is a cloud-based accounting software primarily designed for small businesses, offering tools for invoicing, bank reconciliation, expense tracking, payroll, and financial reporting that can be adapted for small nonprofits. It supports project tracking to simulate basic fund accounting and integrates with donation platforms like Donorbox or Classy. While not nonprofit-specific, its scalability and user-friendly interface make it viable for organizations with straightforward accounting needs.
Pros
- Intuitive, modern interface with excellent mobile app
- Unlimited users on all plans, ideal for volunteer teams
- Strong app marketplace with nonprofit integrations (e.g., fundraising tools)
Cons
- No native fund accounting or grant/donation tracking
- Limited built-in nonprofit reporting (e.g., no Form 990 automation)
- Higher-tier plans required for advanced features like multi-currency
Best For
Small nonprofits with basic accounting needs, volunteer staff, and a preference for cloud-based tools with broad integrations.
Pricing
Starts at $20/month (Starter: basic invoicing), $37/month (Standard: unlimited invoices), up to $70/month (Premium: advanced reporting); nonprofit discounts available.
Wave
otherFree accounting software offering invoicing, expense tracking, and basic reporting ideal for very small nonprofits.
100% free unlimited accounting and invoicing with no subscription fees
Wave is a cloud-based accounting software that provides free invoicing, bookkeeping, receipt scanning, and basic financial reporting primarily for small businesses and freelancers. It allows users to track income, expenses, and generate profit/loss statements without subscription costs for core features. While versatile for simple financial management, it lacks specialized tools for nonprofit fund accounting or donor tracking.
Pros
- Completely free core accounting, invoicing, and reporting features
- Intuitive interface with mobile receipt scanning
- Unlimited users and transactions at no extra cost
Cons
- No fund accounting or grant tracking for nonprofits
- Payment processing incurs transaction fees (2.9% + 30¢)
- Limited reporting and no built-in donor management
Best For
Very small nonprofits with basic bookkeeping needs and tight budgets that don't require specialized fund or compliance features.
Pricing
Free for accounting, invoicing, and reports; 2.9% + 30¢ per credit card transaction; payroll starts at $20/month + $6 per employee (US/Canada).
ZipBooks
otherFree starter accounting tool with invoicing, time tracking, and financial reports suitable for small nonprofit operations.
Beautiful, customizable invoicing with automated reminders and payment processing
ZipBooks is a user-friendly cloud-based accounting platform primarily designed for small businesses, offering invoicing, expense tracking, time tracking, and basic bookkeeping features. For small nonprofits, it handles essential tasks like billing for events, tracking donations as income, and generating simple financial reports. However, it lacks specialized nonprofit tools such as fund accounting, grant tracking, or Form 990 support, making it suitable only for very basic needs.
Pros
- Intuitive interface that's easy for non-accountants
- Free plan with unlimited invoicing and basic reports
- Strong cash flow forecasting and time tracking
Cons
- No dedicated fund accounting or nonprofit-specific reporting
- Lacks donor management or pledge tracking
- Limited integrations for nonprofit CRMs or grant tools
Best For
Very small nonprofits with simple bookkeeping needs, like basic donation tracking and event invoicing, that can't afford specialized software.
Pricing
Free starter plan; Smarter ($15/user/mo); Sophisticated ($35/user/mo); Accountant ($60/user/mo); billed annually.
Zoho Books
specializedAffordable online accounting with project tracking, multi-location support, and automation for growing small nonprofits.
Flexible project and class tracking for approximating nonprofit fund accounting
Zoho Books is a cloud-based accounting platform tailored for small businesses, providing invoicing, expense tracking, bank reconciliation, inventory management, and customizable reporting. For small nonprofits, it supports fund segregation through projects, classes, and tags, along with multi-currency handling and automation for streamlined operations. It integrates well with the Zoho ecosystem and third-party apps, offering scalability without high costs.
Pros
- Affordable pricing with a free tier for low-revenue organizations
- Intuitive interface and mobile app for easy adoption
- Strong automation, workflows, and integrations with Zoho tools
Cons
- Lacks built-in donor management or pledge tracking
- Fund accounting requires custom setups via projects/tags
- Nonprofit-specific reporting (e.g., Form 990) needs manual configuration
Best For
Small nonprofits with basic accounting needs, limited budgets, and existing Zoho ecosystem usage.
Pricing
Free for < $50K annual revenue; paid plans start at $20/org/month (billed annually) for Standard, up to $275 for Ultimate.
FreshBooks
otherIntuitive invoicing and light accounting software with expense management and client portals for small nonprofit teams.
Highly customizable and automated invoicing with recurring billing and late payment reminders
FreshBooks is a cloud-based accounting platform primarily designed for small businesses and freelancers, focusing on invoicing, expense tracking, time tracking, and basic bookkeeping. For small nonprofits, it handles straightforward financial tasks like billing for events or services, managing vendor payments, and generating simple reports. However, it lacks specialized nonprofit tools such as fund accounting, grant tracking, or donor management, making it suitable only for very basic needs.
Pros
- Intuitive interface that's quick to learn for non-accountants
- Strong invoicing and expense tracking for service-based nonprofits
- Mobile app for on-the-go expense capture and approvals
Cons
- No native support for fund accounting or restricted donations
- Limited reporting options for nonprofit compliance and grants
- Lacks integrated donor or pledge management
Best For
Very small nonprofits with minimal accounting needs, such as those focused on basic invoicing for programs or events without complex fund tracking.
Pricing
Starts at $19/month (Simple plan, annually) for 5 clients, up to $60/month (Premium) for unlimited clients; nonprofit discounts may apply via inquiry.
Odoo
enterpriseOpen-source ERP platform with modular accounting, inventory, and nonprofit apps for customizable small organization finance.
Modular app ecosystem enabling seamless addition of nonprofit modules (e.g., donations, events) directly to core accounting without separate systems
Odoo is a versatile open-source ERP platform with a robust accounting module that can be customized for small nonprofits through add-ons for donations, memberships, and events. It provides double-entry accounting, invoicing, bank reconciliation, and financial reporting, integrating seamlessly with CRM and project management tools. While powerful and scalable, it requires configuration to handle nonprofit-specific needs like fund accounting or grant tracking.
Pros
- Highly modular with free community edition and extensive app marketplace
- Strong integration of accounting with nonprofit tools like donations and memberships
- Scalable from basic bookkeeping to full ERP without vendor lock-in
Cons
- Steep learning curve and complex initial setup for non-technical users
- Nonprofit-specific features like advanced fund accounting require customizations
- Overkill for nonprofits needing only simple accounting without ERP extras
Best For
Small nonprofits seeking an affordable, all-in-one ERP that grows with their operations beyond basic accounting.
Pricing
Free open-source Community edition (self-hosted); Enterprise apps from $24/user/month; Odoo Online SaaS and Odoo.sh hosting from $10-25/month base.
Manager
otherFree open-source desktop and cloud accounting software supporting double-entry bookkeeping and custom reports for nonprofits.
Unlimited free usage with no caps on users, transactions, or features in the core edition
Manager.io is a free, open-source desktop accounting software that provides double-entry bookkeeping, invoicing, expense tracking, inventory management, and customizable reporting for small businesses and organizations. It supports unlimited users and transactions without any subscription fees, with an optional cloud version for remote access. While highly flexible for general accounting, it lacks specialized nonprofit features like fund accounting or donor tracking, requiring manual workarounds.
Pros
- Completely free core version with no limits on users, transactions, or companies
- Intuitive interface and straightforward setup with minimal learning curve
- Highly customizable reports, forms, and workflows
Cons
- No built-in fund accounting, grant tracking, or donor management for nonprofits
- Limited integrations with nonprofit-specific tools or CRM systems
- Requires manual customization for compliance like Form 990 reporting
Best For
Budget-constrained small nonprofits with simple cash-based accounting needs that can handle custom setups.
Pricing
Free desktop version; optional cloud hosting from $19/month per organization.
GnuCash
otherFree open-source accounting program with double-entry and multi-account fund tracking for personal and small nonprofit use.
Double-entry accounting with hierarchical charts of accounts for precise financial tracking
GnuCash is a free, open-source desktop accounting application designed for double-entry bookkeeping, suitable for personal finance, small businesses, and basic nonprofit tracking. It supports invoicing, expense tracking, budgeting, payroll, and customizable reports to generate financial statements. While versatile, it requires manual setup for nonprofit-specific needs like fund accounting and lacks cloud integration.
Pros
- Completely free and open-source with no licensing costs
- Robust double-entry accounting ensures accuracy and audit trails
- Highly customizable reports and account structures
Cons
- Steep learning curve, especially for non-accountants
- Desktop-only with no cloud sync or mobile access
- No built-in nonprofit features like fund accounting or donor management
Best For
Tech-savvy small nonprofits or volunteers needing a no-cost, customizable double-entry solution for basic bookkeeping.
Pricing
Free (open-source, donations encouraged)
Conclusion
The review of small nonprofit accounting software highlighted tools that balance specialization and versatility, with Aplos leading as the top choice due to its dedicated features like fund accounting and Form 990 support. QuickBooks Online and Xero stood out as strong alternatives—QuickBooks for its extensive integrations, and Xero for its user-friendly design and customizable reports—ensuring every nonprofit, regardless of size or needs, can find a suitable solution.
Start with Aplos to unlock its tailored nonprofit tools, or explore QuickBooks Online or Xero if their unique strengths better align with your organization’s financial goals—taking the first step toward efficient, effective financial management.
Tools Reviewed
All tools were independently evaluated for this comparison