Quick Overview
- 1#1: Aplos - Cloud-based all-in-one accounting software designed specifically for nonprofits and churches with fund accounting, donor tracking, and budgeting tools.
- 2#2: QuickBooks Nonprofit - Widely-used accounting platform adapted for nonprofits featuring class tracking for funds, donation management, and customizable reporting.
- 3#3: Sage Intacct - Scalable cloud financial management system with advanced fund accounting, grant tracking, and compliance features for mid-sized nonprofits.
- 4#4: Blackbaud Financial Edge NXT - Integrated fund accounting solution combined with CRM for comprehensive financial and fundraising management in large nonprofits.
- 5#5: Oracle NetSuite - Robust cloud ERP platform offering fund accounting, donor stewardship, and real-time analytics tailored for nonprofits.
- 6#6: MIP Advance - Established fund accounting software providing detailed financial tracking, reporting, and regulatory compliance for nonprofits.
- 7#7: Denali Fund - Comprehensive fund accounting system with multi-entity support, payroll integration, and customizable dashboards for nonprofits.
- 8#8: Nonprofit+ - Affordable cloud ERP suite including accounting, CRM, HR, and expense management specifically for small to mid-sized nonprofits.
- 9#9: Xero - User-friendly cloud accounting tool with tracking categories and bank reconciliation suitable for smaller nonprofits.
- 10#10: Wave Accounting - Free basic accounting software for simple nonprofit bookkeeping, invoicing, and receipt scanning.
Tools were chosen based on their ability to address core nonprofit needs like fund accounting, donor tracking, and compliance, alongside factors such as user-friendliness, scalability, and overall value to serve the sector effectively.
Comparison Table
Navigating accounting software tailored for nonprofits can be challenging; this comparison table simplifies the process by featuring top tools like Aplos, QuickBooks Nonprofit, Sage Intacct, Blackbaud Financial Edge NXT, Oracle NetSuite, and more. Readers will gain insights into key factors such as features, pricing, and suitability for various organization sizes to identify the best fit for their needs.
| # | Tool | Category | Overall | Features | Ease of Use | Value |
|---|---|---|---|---|---|---|
| 1 | Aplos Cloud-based all-in-one accounting software designed specifically for nonprofits and churches with fund accounting, donor tracking, and budgeting tools. | specialized | 9.5/10 | 9.8/10 | 9.2/10 | 9.0/10 |
| 2 | QuickBooks Nonprofit Widely-used accounting platform adapted for nonprofits featuring class tracking for funds, donation management, and customizable reporting. | enterprise | 8.6/10 | 8.0/10 | 9.2/10 | 8.3/10 |
| 3 | Sage Intacct Scalable cloud financial management system with advanced fund accounting, grant tracking, and compliance features for mid-sized nonprofits. | enterprise | 8.7/10 | 9.2/10 | 8.0/10 | 8.0/10 |
| 4 | Blackbaud Financial Edge NXT Integrated fund accounting solution combined with CRM for comprehensive financial and fundraising management in large nonprofits. | enterprise | 8.4/10 | 9.2/10 | 7.8/10 | 7.9/10 |
| 5 | Oracle NetSuite Robust cloud ERP platform offering fund accounting, donor stewardship, and real-time analytics tailored for nonprofits. | enterprise | 8.2/10 | 9.1/10 | 7.1/10 | 7.6/10 |
| 6 | MIP Advance Established fund accounting software providing detailed financial tracking, reporting, and regulatory compliance for nonprofits. | enterprise | 8.1/10 | 8.7/10 | 7.4/10 | 7.8/10 |
| 7 | Denali Fund Comprehensive fund accounting system with multi-entity support, payroll integration, and customizable dashboards for nonprofits. | specialized | 7.6/10 | 8.4/10 | 6.8/10 | 7.1/10 |
| 8 | Nonprofit+ Affordable cloud ERP suite including accounting, CRM, HR, and expense management specifically for small to mid-sized nonprofits. | specialized | 8.1/10 | 8.5/10 | 7.9/10 | 8.0/10 |
| 9 | Xero User-friendly cloud accounting tool with tracking categories and bank reconciliation suitable for smaller nonprofits. | other | 7.6/10 | 7.0/10 | 9.2/10 | 8.5/10 |
| 10 | Wave Accounting Free basic accounting software for simple nonprofit bookkeeping, invoicing, and receipt scanning. | other | 6.2/10 | 5.0/10 | 9.3/10 | 9.5/10 |
Cloud-based all-in-one accounting software designed specifically for nonprofits and churches with fund accounting, donor tracking, and budgeting tools.
Widely-used accounting platform adapted for nonprofits featuring class tracking for funds, donation management, and customizable reporting.
Scalable cloud financial management system with advanced fund accounting, grant tracking, and compliance features for mid-sized nonprofits.
Integrated fund accounting solution combined with CRM for comprehensive financial and fundraising management in large nonprofits.
Robust cloud ERP platform offering fund accounting, donor stewardship, and real-time analytics tailored for nonprofits.
Established fund accounting software providing detailed financial tracking, reporting, and regulatory compliance for nonprofits.
Comprehensive fund accounting system with multi-entity support, payroll integration, and customizable dashboards for nonprofits.
Affordable cloud ERP suite including accounting, CRM, HR, and expense management specifically for small to mid-sized nonprofits.
User-friendly cloud accounting tool with tracking categories and bank reconciliation suitable for smaller nonprofits.
Free basic accounting software for simple nonprofit bookkeeping, invoicing, and receipt scanning.
Aplos
specializedCloud-based all-in-one accounting software designed specifically for nonprofits and churches with fund accounting, donor tracking, and budgeting tools.
True nonprofit fund accounting that automatically tracks and reports on restricted, unrestricted, and temporarily restricted funds with multi-fund segmentation.
Aplos is a cloud-based accounting platform designed specifically for nonprofits, churches, and mission-driven organizations, offering fund accounting, donor management, and online giving tools. It provides FASB-compliant reporting, budgeting, payroll integration, and bank reconciliation to streamline financial operations while ensuring compliance with nonprofit standards. With robust security and mobile accessibility, Aplos empowers organizations to focus on their mission rather than manual bookkeeping.
Pros
- Specialized fund accounting for restricted/unrestricted funds
- Integrated donor management and online giving
- Excellent nonprofit-specific reporting and compliance tools
- Strong customer support and training resources
Cons
- Higher pricing tiers can be costly for very small organizations
- Limited advanced customization for complex enterprise needs
- Some integrations require additional setup or fees
Best For
Small to mid-sized nonprofits, churches, and faith-based organizations needing an all-in-one solution for accounting, donations, and reporting.
Pricing
Starts at $59/month (Basic plan) for core accounting; Growth ($99/month) and Pro ($149/month) add advanced features like payroll and unlimited users; custom enterprise pricing available.
QuickBooks Nonprofit
enterpriseWidely-used accounting platform adapted for nonprofits featuring class tracking for funds, donation management, and customizable reporting.
Class and location tracking for simplified multi-fund accounting without needing dedicated nonprofit software.
QuickBooks Nonprofit, offered by Intuit, adapts the popular QuickBooks Online platform for nonprofit organizations with features like class and location tracking to simulate fund accounting. It handles core tasks such as invoicing, expense management, payroll, and bank reconciliations, while enabling customized reports for donors, grants, and compliance. Ideal for smaller nonprofits, it integrates with donor management tools and third-party apps to streamline operations without requiring specialized accounting expertise.
Pros
- Intuitive interface familiar to millions of users
- Extensive app integrations for donor tracking and CRM
- Robust reporting and customization for nonprofit compliance
Cons
- Class-based fund accounting lacks depth for complex multi-fund needs
- No native grant management or pledge tracking
- Pricing can escalate quickly for advanced features
Best For
Small to mid-sized nonprofits seeking user-friendly general accounting with basic fund segmentation and strong integrations.
Pricing
Nonprofit discounts up to 50%; starts at ~$38/month (Simple Start equivalent) up to ~$100/month for Advanced with unlimited funds tracking.
Sage Intacct
enterpriseScalable cloud financial management system with advanced fund accounting, grant tracking, and compliance features for mid-sized nonprofits.
Dimensions for multi-dimensional tracking, enabling precise allocation across funds, grants, programs, and donors without custom coding
Sage Intacct is a robust cloud-based financial management platform tailored for nonprofits, offering true fund accounting, grant management, and donor tracking to meet complex financial needs. It supports multi-entity consolidation, compliance with GAAP and FASB standards, and customizable reporting for nonprofit-specific requirements. The software scales with growing organizations, providing automation for budgeting, forecasting, and endowment management.
Pros
- Advanced fund accounting with unlimited segmentation via Dimensions for tracking by fund, program, or grant
- Seamless multi-entity management and inter-entity transactions
- Powerful dashboards, BI reporting, and nonprofit-specific compliance tools
Cons
- Steep implementation process often requiring certified partners
- Higher cost structure compared to entry-level nonprofit software
- Customization and advanced features demand significant user training
Best For
Mid-to-large nonprofits with complex multi-fund structures, multiple entities, and grant-heavy operations seeking enterprise-grade scalability.
Pricing
Quote-based subscription starting around $15,000-$30,000 annually, varying by modules, users, and nonprofit size.
Blackbaud Financial Edge NXT
enterpriseIntegrated fund accounting solution combined with CRM for comprehensive financial and fundraising management in large nonprofits.
Unlimited dimensional accounting for precise tracking of funds, programs, and grants across multiple entities
Blackbaud Financial Edge NXT is a cloud-based fund accounting platform tailored for nonprofits, enabling precise tracking of restricted funds, grants, endowments, and budgets in compliance with FASB and GAAP standards. It offers advanced reporting, dashboards, and automation for financial management, with seamless integration into Blackbaud's broader ecosystem like Raiser's Edge NXT for fundraising. Designed for complex nonprofit finances, it supports multi-entity organizations with real-time insights and audit-ready reporting.
Pros
- Specialized fund accounting with unlimited segments for nonprofits
- Deep integration with Blackbaud CRM and fundraising tools
- Robust compliance reporting and real-time dashboards
Cons
- High subscription costs for smaller organizations
- Steep learning curve and complex initial setup
- Limited third-party integrations outside Blackbaud ecosystem
Best For
Mid-sized to large nonprofits with complex fund accounting needs and existing Blackbaud tools.
Pricing
Quote-based SaaS pricing, typically $5,000–$20,000+ annually depending on organization size and modules.
Oracle NetSuite
enterpriseRobust cloud ERP platform offering fund accounting, donor stewardship, and real-time analytics tailored for nonprofits.
Multi-dimensional fund accounting enabling simultaneous tracking across unlimited funds, programs, grants, and departments
Oracle NetSuite is a robust cloud-based ERP solution with dedicated nonprofit modules for fund accounting, grant lifecycle management, and constituent relationship management. It offers real-time financial reporting, multi-entity consolidation, and compliance tools tailored to nonprofit standards like FASB and GASB. Designed for scalability, it integrates accounting with CRM, fundraising, and operational workflows to streamline nonprofit operations.
Pros
- Comprehensive fund accounting with unlimited segmentation by fund, grant, and program
- Seamless integration of financials, CRM, and reporting for end-to-end nonprofit management
- Scalable for multi-entity organizations with real-time dashboards and analytics
Cons
- High implementation costs and complexity requiring specialized consultants
- Steep learning curve for non-technical users
- Premium pricing may not suit small nonprofits
Best For
Mid-to-large nonprofits with complex multi-fund operations, grant tracking, and donor management needs.
Pricing
Custom quote-based pricing; typically $15,000-$100,000+ annually depending on users, modules, and nonprofit discounts.
MIP Advance
enterpriseEstablished fund accounting software providing detailed financial tracking, reporting, and regulatory compliance for nonprofits.
Advanced multi-fund and multi-entity accounting engine designed specifically for nonprofit financial complexity
MIP Advance, from Community Brands, is a cloud-based fund accounting software tailored for nonprofits, government agencies, and public sector organizations. It provides core functionalities like general ledger, accounts payable/receivable, payroll, budgeting, and grant tracking, with built-in compliance for FASB and GASB standards. The platform supports multi-entity and multi-fund accounting, integrating seamlessly with other Community Brands tools like NeonCRM for donor management.
Pros
- Robust fund accounting with unlimited funds and segments for complex nonprofit structures
- Strong grant management and compliance reporting tools
- Scalable cloud platform with integrations to CRM and fundraising software
Cons
- Steep learning curve requiring training for full utilization
- Custom pricing can be expensive for smaller organizations
- Limited native mobile app functionality
Best For
Mid-sized nonprofits and public sector entities needing advanced fund accounting and grant compliance.
Pricing
Quote-based pricing starting around $5,000-$10,000 annually, depending on modules, users, and organization size.
Denali Fund
specializedComprehensive fund accounting system with multi-entity support, payroll integration, and customizable dashboards for nonprofits.
Unlimited multi-fund accounting with automatic encumbrance tracking and inter-fund transfers
Denali Fund by Cougar Mountain Software is an on-premise accounting solution tailored for nonprofits, offering robust fund accounting, donor management, grant tracking, and financial reporting to meet FASB and IRS compliance needs. It supports unlimited funds, multi-entity consolidation, and integrates payroll, AP/AR, and inventory modules. Ideal for organizations preferring desktop-based control over their data without cloud dependencies.
Pros
- Comprehensive fund accounting with unlimited funds and real-time allocations
- Highly customizable reports including Form 990 and grant-specific analytics
- Strong integration with donor CRM and payroll for streamlined nonprofit operations
Cons
- On-premise only, requiring local IT setup and maintenance
- Steep learning curve due to desktop interface and complex customization
- High upfront perpetual license costs without SaaS flexibility
Best For
Mid-sized nonprofits that prioritize data security and customization in an on-premise environment over cloud convenience.
Pricing
Perpetual licenses start at $4,000 for core modules, scaling to $15,000-$25,000 for full nonprofit suite, plus 18% annual maintenance.
Nonprofit+
specializedAffordable cloud ERP suite including accounting, CRM, HR, and expense management specifically for small to mid-sized nonprofits.
Unlimited funds and programs with automated allocations and smart rules for precise nonprofit financial tracking
Nonprofit+ by Araize is a cloud-based accounting software tailored for nonprofits, providing true fund accounting, multi-entity management, grant tracking, budgeting, and donor management. It enables organizations to handle complex financial reporting, compliance requirements, and allocations across unlimited funds and programs. The platform integrates with tools like QuickBooks, PayPal, and payroll services, streamlining nonprofit financial operations.
Pros
- True fund accounting with unlimited funds and programs
- Robust grant management and compliance reporting
- Cloud-based accessibility with mobile support
Cons
- Limited native integrations with some CRM tools
- Steeper learning curve for advanced configurations
- Customer support primarily email/ticket-based
Best For
Mid-sized nonprofits requiring dedicated fund accounting, grant tracking, and multi-org capabilities without enterprise-level costs.
Pricing
Starts at $115/month for Starter plan (up to 5 users), $215/month for Professional, $415/month for Enterprise; custom quotes for larger orgs.
Xero
otherUser-friendly cloud accounting tool with tracking categories and bank reconciliation suitable for smaller nonprofits.
Flexible tracking categories that enable organizations to tag and report on multiple funds or projects within a single entity
Xero is a cloud-based accounting software widely used by small to medium nonprofits for core financial management tasks like invoicing, bank reconciliation, expense tracking, and reporting. It leverages tracking categories to approximate fund accounting, allowing organizations to allocate transactions across multiple funds or programs without native multi-fund ledgers. While not purpose-built for nonprofits, its vast app marketplace integrates with donor management tools like Kindful and Bloomerang, enhancing functionality for NFP-specific needs such as grant tracking and fundraising.
Pros
- Highly intuitive interface with minimal learning curve
- Automatic bank feeds and reconciliation save significant time
- Extensive integrations with NFP tools for donors and grants
Cons
- No native fund accounting or multi-fund financial statements
- Advanced NFP reporting requires custom setups or add-ons
- Payroll and compliance features may need third-party extensions
Best For
Small nonprofits with straightforward accounting needs that prioritize ease of use and scalability over specialized fund management.
Pricing
Starts at $15 USD/month (Early plan, annual billing) with up to 75% nonprofit discounts; scales to $70+/month for premium plans including payroll.
Wave Accounting
otherFree basic accounting software for simple nonprofit bookkeeping, invoicing, and receipt scanning.
100% free core accounting tools with no user or transaction limits for basic use
Wave Accounting is a cloud-based, free platform designed primarily for small businesses, providing invoicing, expense tracking, receipt scanning, and basic financial reporting. For nonprofits, it offers straightforward bookkeeping without specialized fund accounting or donor management tools essential for larger NFPs. It's suitable for very small organizations with simple financial needs but falls short on compliance and reporting tailored to nonprofit standards like FASB or Form 990.
Pros
- Completely free core accounting and invoicing features
- Highly intuitive interface with mobile app support
- Unlimited expense tracking and basic reporting
Cons
- Lacks fund accounting, grant tracking, and donor management
- No nonprofit-specific compliance tools or Form 990 support
- Fees for payments and payroll limit full free use
Best For
Very small nonprofits or startups with basic bookkeeping needs and zero budget for software.
Pricing
Free for accounting, invoicing, and reports; payroll from $20/month + $6/employee; 2.9% + $0.60 per credit card transaction.
Conclusion
The reviewed tools present varied solutions to fit different non-profit needs, with Aplos emerging as the top choice—its cloud-based all-in-one design, including fund accounting, donor tracking, and budgeting, making it especially tailored for nonprofits and churches. QuickBooks Nonprofit stands out as a widely used option with customizable reporting and class tracking, while Sage Intacct offers scalable, advanced features like grant tracking, suitable for mid-sized organizations. Both alternatives provide strong options for specific requirements.
Discover how Aplos can streamline your financial operations—try it today to unlock its tailored tools and focus on growing your mission.
Tools Reviewed
All tools were independently evaluated for this comparison