Quick Overview
- 1#1: Aplos - Cloud-based accounting software tailored for nonprofits with fund accounting, donor management, and automated reporting.
- 2#2: QuickBooks Online Nonprofit - Widely-used accounting platform with nonprofit edition featuring fund tracking, budgeting, and Form 990 support.
- 3#3: Sage Intacct - Scalable cloud financial management system with nonprofit-specific modules for grants, funds, and multi-entity accounting.
- 4#4: Blackbaud Financial Edge NXT - Enterprise-grade financial suite for nonprofits integrating accounting, fundraising, and compliance reporting.
- 5#5: MIP Fund Accounting - Robust fund accounting software designed for nonprofits with advanced grant management and audit-ready reports.
- 6#6: Araize Nonprofit+ - All-in-one cloud platform for nonprofit accounting, CRM, and payroll with fund allocation and donor tracking.
- 7#7: AccuFund - Affordable nonprofit accounting solution offering fund accounting, budgeting, and GAAP-compliant financials.
- 8#8: SoftEdge - Nonprofit-focused accounting software with strong reporting, payroll integration, and multi-fund capabilities.
- 9#9: Xero - Cloud accounting tool popular for small nonprofits with app integrations for fund tracking and donations.
- 10#10: Oracle NetSuite - Enterprise ERP system with nonprofit edition for complex fund accounting, grants, and global operations.
Tools were selected based on their alignment with nonprofit requirements—including robust fund accounting, compliance support, and user-friendliness—prioritizing features that drive efficiency, accuracy, and scalability across different organizational sizes.
Comparison Table
This comparison table breaks down key nonprofit accounting software options—including Aplos, QuickBooks Online Nonprofit, Sage Intacct, Blackbaud Financial Edge NXT, MIP Fund Accounting, and more—to help nonprofits identify the right tool. Readers will learn about each solution’s features, pricing, and suitability for different organizational sizes or needs, streamlining the decision-making process for mission-aligned financial management.
| # | Tool | Category | Overall | Features | Ease of Use | Value |
|---|---|---|---|---|---|---|
| 1 | Aplos Cloud-based accounting software tailored for nonprofits with fund accounting, donor management, and automated reporting. | specialized | 9.5/10 | 9.7/10 | 9.2/10 | 9.3/10 |
| 2 | QuickBooks Online Nonprofit Widely-used accounting platform with nonprofit edition featuring fund tracking, budgeting, and Form 990 support. | specialized | 8.8/10 | 8.5/10 | 9.2/10 | 8.6/10 |
| 3 | Sage Intacct Scalable cloud financial management system with nonprofit-specific modules for grants, funds, and multi-entity accounting. | enterprise | 8.7/10 | 9.2/10 | 7.8/10 | 8.1/10 |
| 4 | Blackbaud Financial Edge NXT Enterprise-grade financial suite for nonprofits integrating accounting, fundraising, and compliance reporting. | enterprise | 8.7/10 | 9.2/10 | 7.8/10 | 8.1/10 |
| 5 | MIP Fund Accounting Robust fund accounting software designed for nonprofits with advanced grant management and audit-ready reports. | specialized | 8.2/10 | 9.1/10 | 7.4/10 | 7.9/10 |
| 6 | Araize Nonprofit+ All-in-one cloud platform for nonprofit accounting, CRM, and payroll with fund allocation and donor tracking. | specialized | 8.2/10 | 8.7/10 | 8.0/10 | 7.5/10 |
| 7 | AccuFund Affordable nonprofit accounting solution offering fund accounting, budgeting, and GAAP-compliant financials. | specialized | 8.1/10 | 8.7/10 | 7.2/10 | 7.6/10 |
| 8 | SoftEdge Nonprofit-focused accounting software with strong reporting, payroll integration, and multi-fund capabilities. | specialized | 8.2/10 | 8.7/10 | 7.5/10 | 7.9/10 |
| 9 | Xero Cloud accounting tool popular for small nonprofits with app integrations for fund tracking and donations. | specialized | 7.8/10 | 7.2/10 | 9.1/10 | 8.4/10 |
| 10 | Oracle NetSuite Enterprise ERP system with nonprofit edition for complex fund accounting, grants, and global operations. | enterprise | 8.1/10 | 9.2/10 | 6.8/10 | 7.0/10 |
Cloud-based accounting software tailored for nonprofits with fund accounting, donor management, and automated reporting.
Widely-used accounting platform with nonprofit edition featuring fund tracking, budgeting, and Form 990 support.
Scalable cloud financial management system with nonprofit-specific modules for grants, funds, and multi-entity accounting.
Enterprise-grade financial suite for nonprofits integrating accounting, fundraising, and compliance reporting.
Robust fund accounting software designed for nonprofits with advanced grant management and audit-ready reports.
All-in-one cloud platform for nonprofit accounting, CRM, and payroll with fund allocation and donor tracking.
Affordable nonprofit accounting solution offering fund accounting, budgeting, and GAAP-compliant financials.
Nonprofit-focused accounting software with strong reporting, payroll integration, and multi-fund capabilities.
Cloud accounting tool popular for small nonprofits with app integrations for fund tracking and donations.
Enterprise ERP system with nonprofit edition for complex fund accounting, grants, and global operations.
Aplos
specializedCloud-based accounting software tailored for nonprofits with fund accounting, donor management, and automated reporting.
Advanced fund accounting that automatically handles donor-restricted funds and generates Form 990-ready reports
Aplos is a cloud-based accounting software specifically designed for nonprofits, churches, and faith-based organizations, offering fund accounting, donor management, payroll, and online giving tools. It simplifies compliance with GAAP standards for nonprofits through automated reporting, budgeting, and multi-fund tracking. With seamless integrations and mobile access, Aplos provides real-time financial insights to help organizations manage resources efficiently.
Pros
- True fund accounting for restricted/unrestricted funds with nonprofit-specific compliance
- Integrated donor management and online giving platform
- Excellent customer support and intuitive dashboard for non-accountants
Cons
- Higher pricing tiers for advanced features may strain very small nonprofits
- Limited third-party integrations compared to general accounting software
- Payroll add-on requires separate setup and additional cost
Best For
Small to mid-sized nonprofits, churches, and ministries needing an all-in-one solution for fund accounting and donor tracking.
Pricing
Starts at $59/month for basic accounting (billed annually), with Professional at $99/month and Enterprise custom; add-ons like payroll extra.
QuickBooks Online Nonprofit
specializedWidely-used accounting platform with nonprofit edition featuring fund tracking, budgeting, and Form 990 support.
Unlimited class and location tracking for precise multi-fund nonprofit accounting
QuickBooks Online Nonprofit is a cloud-based accounting platform customized for nonprofit organizations, enabling fund accounting, donor management, and grant tracking. It supports multiple funds via class and location tracking, automates pledge and donation processing, and generates essential reports like Form 990 for compliance. With bank feed integrations and mobile access, it simplifies financial management for nonprofits of varying sizes.
Pros
- Intuitive, familiar interface with minimal learning curve
- Strong fund accounting and donor/pledge tracking capabilities
- Seamless integrations with banks, payment processors, and CRM tools
Cons
- Lacks some advanced nonprofit-specific features like endowment management
- Subscription pricing can escalate for larger organizations
- Custom reports may require setup or accountant assistance
Best For
Small to mid-sized nonprofits needing user-friendly, scalable accounting with reliable general ledger and basic fund tracking.
Pricing
Nonprofit discounts (up to 30-50% off): Plus plan ~$65/month, Advanced ~$140/month (annual billing; prices vary by promotion).
Sage Intacct
enterpriseScalable cloud financial management system with nonprofit-specific modules for grants, funds, and multi-entity accounting.
Multi-dimensional fund accounting that simultaneously tracks transactions across unlimited dimensions like fund, program, grant, and location for unparalleled nonprofit visibility.
Sage Intacct is a robust cloud-based financial management platform tailored for nonprofits, providing specialized fund accounting, grant lifecycle management, and donor tracking to ensure compliance with nonprofit GAAP standards. It offers real-time dashboards, multidimensional reporting, and multi-entity consolidation for organizations managing multiple funds or locations. The software excels in scalability, integrating seamlessly with CRM systems like Salesforce for streamlined operations.
Pros
- Advanced fund accounting with multi-dimensional tracking for funds, programs, grants, and departments
- Powerful real-time reporting and customizable dashboards for nonprofit-specific insights
- Strong integrations with CRM and fundraising tools like Salesforce and Classy
Cons
- Steep learning curve and complex setup requiring training or consultants
- High pricing that may be prohibitive for small nonprofits
- Limited out-of-the-box templates for very niche nonprofit workflows
Best For
Mid-sized to large nonprofits with complex multi-fund operations, grant management, and growth ambitions requiring enterprise-grade scalability.
Pricing
Quote-based; typically starts at $15,000–$30,000 annually for nonprofit configurations, scaling with users, entities, and modules.
Blackbaud Financial Edge NXT
enterpriseEnterprise-grade financial suite for nonprofits integrating accounting, fundraising, and compliance reporting.
Native, unlimited fund accounting with real-time grant tracking and automated allocation rules
Blackbaud Financial Edge NXT is a cloud-based fund accounting software tailored for nonprofits, offering robust tools for financial management, budgeting, and reporting compliant with nonprofit standards like FASB. It excels in handling complex fund accounting across multiple entities and integrates seamlessly with Blackbaud's CRM solutions like Raiser's Edge NXT for streamlined donor and grant tracking. The platform provides real-time dashboards, automated workflows, and audit-ready reporting to support nonprofit financial operations efficiently.
Pros
- Specialized fund accounting for nonprofits with multi-entity support
- Seamless integration with Blackbaud CRM and fundraising tools
- Advanced reporting and compliance features for audits and grants
Cons
- Steep learning curve for new users
- Higher pricing suitable for mid-to-large organizations only
- Customization often requires professional services
Best For
Mid-sized to large nonprofits needing integrated fund accounting with donor management and grant compliance.
Pricing
Quote-based subscription pricing, typically $15,000–$50,000+ annually based on organization size, users, and modules.
MIP Fund Accounting
specializedRobust fund accounting software designed for nonprofits with advanced grant management and audit-ready reports.
Unlimited fund, segment, and object accounting for granular tracking of restricted funds and grants without limitations
MIP Fund Accounting, offered by Community Brands, is a robust financial management software designed specifically for nonprofits, government agencies, and organizations handling grants and funds. It provides true fund accounting with unlimited funds, segments, and objects, enabling precise tracking of restricted and unrestricted resources. The platform supports budgeting, grant management, payroll integration, and customizable reporting to ensure compliance with FASB, GASB, and other standards.
Pros
- Exceptional fund accounting with unlimited dimensionality for complex nonprofit finances
- Strong compliance reporting and grant lifecycle management tools
- Scalable with integrations to CRM, HR, and fundraising software
Cons
- Dated user interface that may require training
- Lengthy implementation and customization process
- Higher pricing suitable for larger organizations only
Best For
Mid-to-large nonprofits and public sector entities with complex multi-fund accounting and grant tracking requirements.
Pricing
Custom quote-based pricing starting around $10,000-$20,000 annually depending on modules, users, and deployment (on-premise or cloud).
Araize Nonprofit+
specializedAll-in-one cloud platform for nonprofit accounting, CRM, and payroll with fund allocation and donor tracking.
Seamless integration of fund accounting with built-in donor CRM for real-time relationship insights
Araize Nonprofit+ is a cloud-based accounting software tailored for nonprofits, offering fund accounting, donor management, grant tracking, and budgeting tools in an integrated platform. It handles complex nonprofit financial needs like restricted fund tracking, pledge management, and compliance reporting while incorporating CRM functionality for donor relationships. The solution supports multi-entity organizations with real-time dashboards and mobile access for streamlined operations.
Pros
- Robust fund accounting with multi-fund support
- Integrated donor CRM and pledge tracking
- Strong grant management and compliance reporting
Cons
- Pricing can be steep for very small nonprofits
- Limited third-party integrations
- Interface feels dated compared to modern competitors
Best For
Mid-sized nonprofits needing an all-in-one accounting and donor management solution without heavy customization.
Pricing
Subscription starts at ~$115/month for basic plans, scaling to $500+/month for enterprise with custom quotes based on users and features.
AccuFund
specializedAffordable nonprofit accounting solution offering fund accounting, budgeting, and GAAP-compliant financials.
Unlimited fund segmentation with real-time balance tracking and automatic compliance enforcement
AccuFund is a robust on-premises fund accounting software tailored for nonprofits, government agencies, and organizations with complex grant and fund management needs. It excels in tracking multiple funds simultaneously, ensuring compliance with grant requirements, and producing detailed financial reports. The platform supports budgeting, payroll integration, accounts payable/receivable, and multi-entity consolidation for streamlined operations.
Pros
- Powerful multi-fund accounting with unlimited segmentation
- Advanced grant tracking and compliance tools
- Highly customizable reporting and audit-ready outputs
Cons
- On-premises only, lacking cloud/SaaS flexibility
- Steep learning curve and lengthy implementation
- High upfront costs unsuitable for small nonprofits
Best For
Mid-to-large nonprofits and government entities requiring sophisticated fund accounting and grant compliance.
Pricing
Custom quote-based; perpetual licenses start at ~$8,000-$20,000+ depending on modules, plus annual maintenance (~20% of license cost).
SoftEdge
specializedNonprofit-focused accounting software with strong reporting, payroll integration, and multi-fund capabilities.
Advanced grant management that automates tracking from application through expenditure reporting and reimbursement.
SoftEdge is a cloud-based fund accounting software designed specifically for nonprofits, offering tools for multi-fund tracking, grant management, and donor contributions. It supports GAAP and FASB compliance with customizable reporting, budgeting, and payroll integration tailored to mission-driven organizations. The platform emphasizes scalability for growing nonprofits while providing real-time financial insights.
Pros
- Robust fund accounting with multi-entity support
- Comprehensive grant lifecycle tracking and compliance reporting
- Seamless integration with payroll and donor management systems
Cons
- Steep learning curve for users new to fund accounting
- Custom pricing can be expensive for small nonprofits
- Limited mobile app functionality compared to competitors
Best For
Mid-sized nonprofits with complex grant funding and multi-fund budgeting requirements.
Pricing
Quote-based pricing starting at approximately $500/month for basic plans, scaling with user count and modules.
Xero
specializedCloud accounting tool popular for small nonprofits with app integrations for fund tracking and donations.
Unlimited users included in all plans, enabling team collaboration without extra costs
Xero is a cloud-based accounting platform that provides small businesses and nonprofits with tools for invoicing, expense tracking, bank reconciliation, and financial reporting. For nonprofits, it supports basic fund accounting through tracking categories, multi-currency handling, and customizable reports, though it lacks deep specialization in donor management or grant compliance. It integrates with third-party apps like Donorbox for enhanced nonprofit functionality, making it suitable for smaller organizations transitioning from spreadsheets.
Pros
- Intuitive interface with mobile app access
- Automated bank feeds and unlimited users
- Strong integrations with nonprofit tools like Donorbox
Cons
- No native fund accounting or donor CRM
- Limited built-in nonprofit reporting templates
- Advanced features require higher pricing tiers
Best For
Small to mid-sized nonprofits needing user-friendly general accounting with basic fund tracking and scalability.
Pricing
Starts at $15 USD/month (Early plan, annually billed) up to $78/month (Established); nonprofit discounts and free trial available.
Oracle NetSuite
enterpriseEnterprise ERP system with nonprofit edition for complex fund accounting, grants, and global operations.
Advanced multi-fund accounting with real-time consolidation across entities
Oracle NetSuite is a cloud-based ERP system offering robust financial management for nonprofits via its Nonprofit Starter Edition and specialized modules. It excels in fund accounting, grant lifecycle management, donor tracking, and compliance reporting aligned with FASB and GAAP standards. The platform integrates CRM, analytics, and operational tools to support scaling nonprofit operations seamlessly.
Pros
- Comprehensive fund accounting with multi-dimensional tracking
- Scalable enterprise-grade integrations for CRM and reporting
- Strong compliance tools for grants and donor management
Cons
- High implementation costs and complexity
- Steep learning curve for non-technical users
- Premium pricing not ideal for small nonprofits
Best For
Mid-to-large nonprofits requiring integrated ERP with advanced fund accounting and growth scalability.
Pricing
Quote-based; Nonprofit Starter Edition starts around $10,000-$20,000 annually plus implementation fees.
Conclusion
The top three nonprofit accounting software tools each bring unique value: Aplos leads as the top choice with its tailored design for nonprofits, QuickBooks Online Nonprofit remains a trusted option with strong Form 990 support, and Sage Intacct excels for scalable, complex operations. This ranking caters to diverse needs, from small groups to enterprise-level organizations, ensuring the right fit for every mission.
Explore Aplos today to streamline your nonprofit’s accounting, enhance fund tracking, and focus on what matters most—your cause. It’s the top tool for those seeking a blend of power and simplicity.
Tools Reviewed
All tools were independently evaluated for this comparison