10 Best Nonprofit Accounting Software

Best Nonprofit Accounting Software refers to specialized financial management tools designed to meet the unique needs of nonprofit organizations, such as fund tracking, donation management, grant reporting, and compliance with nonprofit accounting standards. Unlike generic accounting software, the best nonprofit options offer features like fund accounting, donor management integration, budgeting by project or program, and nonprofit-specific financial reporting (e.g., Statements of Activities and Functional Expenses). These tools ensure transparency, improve financial stewardship, and streamline audits and reporting. Leading software like QuickBooks Nonprofit, Aplos, and ParishSOFT are widely recognized for helping nonprofits maintain compliance, manage restricted funds accurately, and build trust with donors and board members through clear, organized financial records.

The 10 best nonprofit accounting software are listed below.

• ParishSOFT: ParishSOFT is a church management and accounting software designed specifically for Catholic parishes and dioceses, offering tools like fund accounting, contribution tracking, and integrated parish operations. It ensures compliance with nonprofit financial standards and improves stewardship by organizing finances transparently and securely.
• QuickBooks: QuickBooks (Nonprofit version) is an intuitive accounting software that helps nonprofits track donations, generate financial reports, and manage expenses with ease. It offers customizable templates for Statements of Financial Position and Activities, making reporting clear and compliant.
• GMS Accounting: GMS Accounting is a nonprofit-focused software that supports grant-funded organizations with strong tools for cost allocation, fund tracking, and federal reporting. It's tailored to meet the needs of government and nonprofit agencies managing multiple funding sources.
• Xero: Xero is a cloud-based accounting software that offers real-time financial tracking, bank reconciliation, and user-friendly dashboards. While not nonprofit-specific, it provides robust tools for budgeting and reporting that suit small to mid-sized nonprofit organizations.
• Aplos: Aplos is built specifically for nonprofits and churches, offering fund accounting, donation tracking, and nonprofit reporting in one platform. Its simplicity and nonprofit-specific features make it ideal for organizations without professional accounting staff.
• Cougar Mountain Denali Fund: Cougar Mountain Denali Fund is a modular accounting software designed for nonprofits, offering features like fund tracking, GAAP-compliant reporting, and strong internal controls. It is known for handling complex fund structures while maintaining audit readiness.
• File 990: File 990 is a cloud-based solution that allows nonprofits to quickly and accurately file IRS Form 990-N and 990-EZ. It simplifies compliance and reduces filing errors with a guided process tailored for nonprofit reporting needs.
• Fund EZ: Fund EZ is nonprofit accounting software focused on simplifying fund accounting, budgeting, and financial reporting. It supports grant management and program-based accounting to ensure accurate tracking of restricted and unrestricted funds.
• MIP Fund Accounting: MIP Fund Accounting is a powerful accounting system designed for nonprofits and government entities, offering customizable modules for budgeting, payroll, and grant tracking. It excels in managing complex financial structures and ensuring compliance with nonprofit standards.
• Serenic Navigator: Serenic Navigator is an advanced fund accounting solution built on Microsoft Dynamics, designed for larger nonprofits, NGOs, and government agencies. It includes robust grant management.

1. ParishSOFT

ParishSOFT is church-focused accounting and management software tailored for Catholic parishes and dioceses, offering built-in fund accounting, donation tracking, pledge reporting, and parishioner databases. Key nonprofit accounting features include tracking restricted/unrestricted funds, generating IRS-compliant giving statements, and integrated financial reporting within a single platform. Pricing ranges from approximately $19 to $49 per month depending on volume or plan. Users report it is fairly intuitive, though some find the interface dated and occasional lag issues exist. Customer service receives praise for being responsive and helpful. Pros: unified parish and financial management, strong support, tailored to Catholic needs; Cons: outdated look, occasional user errors in fund allocation, limited WordPress integration.

2. QuickBooks

QuickBooks for nonprofits is an intuitive, widely used accounting platform adapted with nonprofit-specific templates and reporting tools. It supports fund tracking, donation entry, and generation of Statement of Activities and Financial Position compatible with IRS requirements. Pricing typically starts around $99/month for QuickBooks Online Plus, with discounted nonprofit rates via TechSoup (~$75-$160/year) for qualified organizations. Users find the interface familiar and easy to learn, though some smaller nonprofits may find it more than they need; strong customer support and rich help resources are often cited as strengths. Pros: widespread adoption, flexible add-ons, easy tax compliance; Cons: higher cost than budget alternatives, manual setup for fund accounting.

3. GMS

GMS Accounting is an on-premise solution built specifically for nonprofits and public sector organizations managing grant and contract funding. Its nonprofit features include advanced fund accounting, grant tracking, cost allocation for shared expenses, and detailed project-based reporting. Pricing is customized and generally tailored to medium/large organizations; GMS provides specialized installation and professional training on-site. User feedback highlights strong financial control, federal compliance support, and responsive customer service. Pros: ideal for grant-heavy nonprofits, robust reporting, comprehensive support; Cons: not cloud-based, steeper implementation and cost.

4. Xero

Xero is cloud-based accounting software with clean design and real-time financial dashboards—but not specifically built for nonprofits. It supports general needs like bank reconciliation, expense tracking, and reporting, though fund accounting needs to be manually configured. Pricing starts low (e.g. ~$20-30/month) making it accessible to small nonprofits. Users like its ease of use and mobility, though nonprofit-specific metrics require customization. Customer support is moderate. Pros: affordable, user-friendly; Cons: lacks native nonprofit fund tools and donation modules.

5. Aplos

Aplos is a cloud-native accounting solution built exclusively for nonprofits and churches, offering features like fund accounting, donation management, grant tracking, and nonprofit-specific reports. Pricing is often in the $59-$79/month range with higher tiers (~$179/month) for advanced needs. Users describe its interface as intuitive and well-structured, requiring minimal accounting knowledge, and praise its strong customer service and training resources. Pros: nonprofit-focused, ease of use, excellent support; Cons: limited customization, moderate scalability, slightly higher cost than basic options.

6. Cougar Mountain

Cougar Mountain Denali is a robust modular accounting system designed for nonprofits, offering fund- and project-based accounting, GAAP-compliant reporting, and internal controls. It handles complex fund structures and supports audit readiness. Pricing is custom and often suited for mid-to-large organizations. Users value its flexibility and strong reporting but note the learning curve is steeper, and setup can be complex. Customer service quality varies by partner.

7. File 990

File 990 is a streamlined cloud-based tool focused on preparing and filing IRS Forms 990-N, 990-EZ, and 990-PF for nonprofits. It simplifies compliance with guided workflows, minimizing errors in filing. Pricing is tiered based on form type and organization size. Users find it efficient for filing, with limited accounting features—customer support is responsive but focused primarily on 990 matters. Pros: easy tax filing, low cost; Cons: no full accounting or fund tracking capabilities.

8. Fund EZ

Fund EZ is a nonprofit accounting system built to simplify fund accounting, budgeting, and program-based reporting. It supports grant and restricted fund tracking and offers modules for financial oversight. Pricing is generally moderate and fixed, with support included. The user experience is straightforward, and customer service is focused. Pros: structured for fund accounting, easy budgeting; Cons: less widely adopted, fewer integrations.

9. MIP Fund Accounting

MIP Fund Accounting is an enterprise-level nonprofit financial management system featuring fund accounting, budgeting, payroll, and grant tracking. It is known for handling sophisticated financial operations of large nonprofits and government entities. Pricing is custom and typically higher-end. Users appreciate its scalability and compliance features but note implementation complexity and cost. Support is considered strong based on agency-level service.

10. Serenic Navigator

Serenic Navigator is a full-featured ERP-style software for larger nonprofits and NGOs, including grant and fund accounting, budgeting, and global business rules. It integrates tightly with Microsoft Dynamics environments and supports advanced financial tracking, dashboards, and encumbrance reporting. Pricing is enterprise-level and requires direct vendor consultation. Users praise its dashboard flexibility, data import/export tools, and technical support. Pros: highly capable, scalable, and audit-ready; Cons: expensive, complex implementation, steeper learning curve.

How to Choose Nonprofit Accounting Software?

To choose nonprofit accounting software, follow the steps below.

1. Identify Your Organization's Size and Needs. Small nonprofits may only need basic fund tracking; larger organizations may require grant management, budgeting, or donor CRM integration.
2. Ensure the software supports fund-based accounting, allowing you to separate restricted, unrestricted, and temporarily restricted funds.
3. Choose platforms that generate IRS Form 990 reports and audit-ready financial statements (Statement of Activities, Statement of Financial Position).
4. Look for customizable reporting, multi-program budgeting, and the ability to export reports for board members or grantors.
5. Ensure the software integrates with donation platforms, CRMs, payroll systems, or church management software if needed.
6. Choose a solution that fits your budget now but can scale as your nonprofit grows.
7. Opt for software with good user onboarding, support resources, and responsive customer service.
8. Prioritize Cloud-Based and Security Features by ensuring accessibility and data backups; check for secure login, user permissions, and encryption.

What are the Features of Nonprofit Accounting Software?

The features of nonprofit accounting software are listed below.

• Fund Accounting: Tracks multiple funds separately (e.g., grants, donations, programs).
• Donation Management: Records contributions, donor history, and recurring gifts.
• Grant Tracking: Manages grant cycles, allocations, and financial reporting.
• Budgeting Tools: Allows budget creation and comparison across departments/programs.
• IRS Form 990 Preparation: Generates reports needed for tax filing and compliance.
• Financial Reports: Creates Statements of Activities, Position, and Functional Expenses.
• Multi-User Access with Permissions: Enables secure access for staff and board.
• Audit Trail and Internal Controls: Tracks every transaction for accountability.
• Integration with CRMs/Payroll/Bank Feeds: Streamlines data management.
• Customizable Dashboards and Reports: Tailors views for leadership or departments

How much does Nonprofit Accounting Software cost?

Nonprofit accounting software typically costs between $30 to $300+ per month, depending on the features, organization size, and whether it is cloud-based or on-premise. Basic platforms like Wave or ZipBooks may offer free or low-tier plans under $30/month. Mid-range options like Aplos or QuickBooks for Nonprofits range from $59 to $179/month, depending on donation tools and fund tracking needs. Enterprise-level software such as MIP Fund Accounting or Serenic Navigator can cost several hundred to thousands per year, often based on user seats, modules, and support levels. Many providers offer nonprofit discounts, especially when accessed via TechSoup or direct nonprofit pricing programs.

Is there a Free Nonprofit Accounting Software?

Yes, there are free nonprofit accounting software options, though they come with limited functionality compared to paid tools. For example, Wave Accounting offers free general accounting features that can be customized for nonprofits, though it lacks true fund accounting and donor management. ZipBooks and Odoo (Community Edition) are also viable options for basic bookkeeping. These platforms are best suited for very small nonprofits or those with in-house accounting expertise. However, they do not offer built-in support for fund restrictions, grant tracking, or 990 filing, which are critical for nonprofit compliance. Therefore, free options are helpful for startups, but most established nonprofits eventually transition to paid software.

Can Nonprofit Accounting Software be used for For-Profit Accounting?

Nonprofit accounting software is not ideal for for-profit businesses because it is specifically built to handle fund accounting, donor restrictions, and compliance with nonprofit-specific regulations (e.g., IRS Form 990, FASB 117 reporting). These platforms typically lack features important to for-profits, such as inventory management, profit/loss tracking, sales tax handling, and income reporting focused on shareholder interests. While it's technically possible to use nonprofit software for basic transactions, it would result in inefficient workflows, incorrect financial reporting, and potentially noncompliant statements for taxation or investors. For-profits should use software tailored to GAAP business accounting standards, such as QuickBooks, Xero, or FreshBooks (for commercial enterprises).