5 Best Accounting Software for Non Profits: Low Cost, Key Features

Managing finances for a nonprofit organization involves unique challenges, from tracking restricted funds and managing grants to ensuring compliance with reporting standards. The right accounting software can streamline these processes, enhancing financial transparency, simplifying budgeting, and improving donor management. In this article, we’ll explore the top five accounting software solutions for nonprofits in 2025, highlighting their key features, pros and cons, and the specific needs they address. Whether you’re a small charity or a large nonprofit organization, this guide will help you find the best tool to support your mission and financial goals.

Key Criteria When Evaluating

1. Fund Accounting Capabilities

Nonprofits often manage multiple funds, each with its own restrictions and reporting requirements. The software should:

• Support Restricted and Unrestricted Funds: Ability to track and report on funds designated for specific programs or purposes.
• Enable Program-Based Accounting: Provide insights into the financial performance of individual programs or projects.
• Offer Customizable Chart of Accounts: Allow for categorization of income and expenses to meet specific reporting needs.

2. Budgeting and Financial Planning Tools

Effective budgeting is critical for nonprofits to ensure resources are allocated efficiently:

• Scenario Planning: Features that allow nonprofits to model different budget scenarios and forecast financial outcomes.
• Grant Budget Management: Tools to create and monitor budgets tied to specific grants or funding sources.
• Automated Budget Tracking: Real-time tracking of expenses against the budget with alerts for budget overruns.

3. Donation and Grant Management

Nonprofits rely heavily on donations and grants, requiring specialized tools for:

• Donor Management: CRM (Customer Relationship Management) features to track donor information, manage communication, and analyze donor trends.
• Grant Tracking: Tools to monitor grant application status, compliance requirements, and grant-specific financial reporting.
• Recurring Donation Support: Ability to manage pledges and automate recurring donations to improve cash flow.

4. Reporting and Compliance Features

Compliance with accounting standards and regulatory requirements is critical:

• Pre-Built Compliance Reports: Automated generation of IRS Form 990 and other required financial reports.
• Customizable Reports: Ability to create tailored financial statements for board members, grant providers, and donors.
• Audit Trail Management: Maintain detailed records of financial transactions for audit purposes.

5. Ease of Use and Accessibility

The software should be user-friendly and accessible to all staff members, including those with limited accounting experience:

• Intuitive Interface: Simplified navigation and data entry to reduce training needs.
• Cloud-Based Accessibility: Allow remote access to financial data and facilitate collaboration among team members.
• Mobile Compatibility: Support for mobile devices to enable on-the-go management of financial tasks.

6. Integration with Other Tools

Nonprofits often use a variety of software for operations, fundraising, and communications:

• CRM Integration: Sync donor data seamlessly with donor management systems like Salesforce or DonorPerfect.
• Payment Processing Integration: Connect with tools like PayPal or Stripe for donation collection.
• Project Management Integration: Link financial data with project management tools for streamlined budgeting and reporting.

7. Scalability and Flexibility

As nonprofits grow, their financial management needs may change:

• Support for Growing Organizations: Choose software that can handle increasing transaction volumes and expanding programs.
• Modular Features: Ability to add new functionalities, such as advanced reporting or payroll services, as needed.
• Customization Options: Adapt the software to meet specific nonprofit needs, such as creating custom reports or adding user-defined fields.

8. Pricing and Value for Money

Nonprofits must be mindful of their budgets and ensure they receive good value:

• Affordable Pricing Models: Look for tiered pricing, special nonprofit discounts, or grant-funded software programs.
• Transparent Fees: Avoid software with hidden costs for additional features, user licenses, or support services.
• Free Trials and Demos: Take advantage of free trials to test the software’s features before committing to a purchase.

It is these criteria that we used to establish this list of the best accounting software for non-profits. Here are the results:

#1. QuickBooks Nonprofit

QuickBooks Nonprofit, part of Intuit’s QuickBooks suite, is tailored specifically for nonprofit organizations. It offers powerful accounting tools with nonprofit-specific features, making it an ideal choice for small to mid-sized nonprofits.

Key Features:

• Fund Accounting: Easily manage restricted and unrestricted funds.
• Donation Tracking: Track donations and generate donor acknowledgment letters.
• Grant Management: Monitor grant expenses and ensure compliance.
• Reporting Tools: Pre-built and customizable reports, including IRS Form 990.

Pros:

• User-friendly interface with a shallow learning curve.
• Affordable pricing and discounts for nonprofits.
• Strong integration with popular apps like PayPal, Salesforce, and MailChimp.

Cons:

• Limited advanced features for larger organizations.
• Some users may find the reporting tools less customizable compared to higher-end solutions.

Best For:

• Small to mid-sized nonprofits seeking a balance of features and affordability.

Pricing: Specific pricing details for QuickBooks Nonprofit are not provided in the available sources.

#2. Aplos Accounting

Aplos Accounting is designed exclusively for nonprofits and churches, focusing on simplifying fund accounting, donor management, and financial reporting.

Key Features:

• Fund Accounting: True fund accounting with automatic tracking of designated funds.
• Donor Management: Built-in CRM for managing donor data and communication.
• Budgeting Tools: Create, track, and adjust budgets with ease.
• Event Management: Tools for event registration and ticketing.

Pros:

• Comprehensive nonprofit-specific features in one platform.
• Strong donor management and communication tools.
• Easy integration with payment processors and email marketing tools.

Cons:

• Limited advanced features for very large nonprofits.
• Fewer integrations with third-party software compared to some competitors.

Best For:

• Small to medium-sized nonprofits needing strong donor management and fundraising tools.

Pricing:

• Lite Plan: $79 per month (or $59.25 per month if billed annually), includes fund accounting, donation tracking, online giving forms, financial and giving reports, and event registration.
• Core Plan: $99 per month (or $74.25 per month if billed annually), includes all Lite Plan features plus budgeting, accounts payable and receivable.
• Advanced Plan: Customized solutions starting at $189 per month, designed for organizations tracking budgets and financials for grants, programs, departments, or multiple locations.

#3. Blackbaud Financial Edge NXT

Blackbaud Financial Edge NXT is a robust cloud-based accounting solution for large nonprofits and organizations with complex financial needs.

Key Features:

• Advanced Fund Accounting: Manage multiple funds and grants with ease.
• Budgeting and Forecasting: Powerful tools for financial planning and scenario analysis.
• Built-In Compliance Tools: Ensure adherence to FASB, GAAP, and IRS requirements.
• Customizable Dashboards: Provide insights for management and board members.

Pros:

• Highly scalable with advanced features for complex needs.
• Strong reporting tools, including custom report creation and audit trails.
• Integrates seamlessly with other Blackbaud products for holistic nonprofit management.

Cons:

• Higher price point may be prohibitive for smaller organizations.
• Steeper learning curve due to its advanced features.

Best For:

• Large nonprofits or organizations managing multiple programs and funding sources.

Pricing: Specific pricing details are not provided in the available sources. However, it is noted that Blackbaud Financial Edge NXT is a complex and expensive system that requires significant customization and training to use effectively.

#4. Sage Intacct Nonprofit

Sage Intacct Nonprofit offers a powerful, cloud-based financial management solution that focuses on improving transparency, efficiency, and compliance for nonprofits.

Key Features:

• Fund and Grant Accounting: Track funds, manage grants, and automate compliance reporting.
• Real-Time Financial Reporting: Access up-to-date financial data and insights.
• Budgeting and Planning: Advanced tools for managing budgets and forecasting.
• Multi-Entity Management: Ideal for organizations with multiple locations or programs.

Pros:

• Excellent reporting features with customizable dashboards.
• Strong compliance support, including audit-ready financials.
• Flexible and scalable for growing nonprofits.

Cons:

• Higher cost compared to simpler solutions.
• May require training to fully utilize its advanced features.

Best For:

• Medium to large nonprofits that need advanced financial management and reporting capabilities.

Pricing: Specific pricing details are not provided in the available sources.

#5. Fund EZ

FundEZ is a comprehensive accounting software designed specifically for nonprofit organizations. It offers a range of features to manage fund accounting, budgeting, and financial reporting, aiming to simplify financial management for nonprofits of various sizes.

Key Features:

• Fund Accounting: Allows tracking of multiple funds, grants, and programs, ensuring compliance with nonprofit accounting standards.
• Budgeting: Provides tools for creating and managing budgets, including comparisons between actual and budgeted figures.
• Financial Reporting: Generates standard and custom financial reports, facilitating transparency and informed decision-making.
• Accounts Payable and Receivable: Manages vendor payments and donor contributions efficiently.
• Payroll Integration: Integrates with payroll systems to streamline employee compensation processes.

Pros:

• User-Friendly Interface: Designed with nonprofits in mind, making it accessible for users with varying levels of accounting expertise.
• Scalability: Suitable for small to medium-sized nonprofits, with features that can accommodate organizational growth.
• Compliance: Ensures adherence to nonprofit accounting standards and regulations.

Cons:

• Limited Advanced Features: May lack some advanced functionalities required by larger organizations with complex accounting needs.
• Integration Limitations: Integration with third-party applications might be limited compared to the other solutions on our list.

Best Suited For: Small to medium-sized nonprofit organizations in the United States seeking an affordable and straightforward accounting solution tailored to their specific financial management needs.

Pricing: Specific pricing details for FundEZ are not readily available.

Comparison Table

Software	Best For	Key Features	Pricing	Pros	Cons
QuickBooks Nonprofit	Small nonprofits & startups	Fund accounting, donation tracking, basic grant management	Starts at $55/month	Easy to use, widely adopted, strong donor management	Limited advanced features, fewer integrations
Aplos Accounting	Faith-based & smaller nonprofits	True fund accounting, donor management, event registration	Starts at $59/month	Built-in CRM, intuitive interface, good for churches	Limited for larger organizations
Sage Intacct Nonprofit	Mid-sized to large nonprofits	Advanced fund accounting, grant & expense management, reporting	Custom pricing (quote-based)	Highly scalable, strong reporting tools	Higher cost, steeper learning curve
Blackbaud Financial Edge NXT	Large, complex nonprofits	Comprehensive grant management, FASB compliance, reporting	Custom pricing (quote-based)	Powerful analytics, audit-ready, great support	Expensive, setup can be complex
Fund EZ	Small to medium-sized U.S. nonprofits needing affordable, straightforward financial management	Fund accounting, budgeting, financial reporting, accounts payable/receivable, payroll integration	Custom pricing (quote-based)	User-friendly interface, scalable for small to medium nonprofits, ensures compliance with nonprofit standards	Limited advanced features for large organizations, fewer third-party integrations

Recommendations Based on Nonprofit Sizes and Types

1. Small Nonprofits and Startups

• Recommended Software: QuickBooks Nonprofit or Aplos Accounting
• Why? These platforms are affordable, easy to use, and provide essential features like fund accounting and donor management without overwhelming smaller organizations.

2. Medium-Sized Nonprofits

• Recommended Software: Sage Intacct Nonprofit
• Why? It offers a strong balance of advanced features, reporting tools, and scalability. As nonprofits grow, Sage Intacct can support additional needs without requiring a transition to new software.

3. Large Nonprofits with Complex Needs

• Recommended Software: Blackbaud Financial Edge NXT or Nonprofit+
• Why? These platforms provide robust tools for managing multiple funds, handling complex grant requirements, and generating highly customizable reports. They also offer strong compliance support and audit trail features.

4. Faith-Based Organizations and Churches

• Recommended Software: Aplos Accounting
• Why? Aplos offers specific features for managing tithes, donations, and event registration, making it ideal for churches and faith-based groups.

5. Nonprofits Heavily Dependent on Grants

• Recommended Software: Nonprofit+ or Sage Intacct Nonprofit
• Why? Both platforms offer advanced grant management tools, including the ability to track grant funds separately and automate grant-specific reporting.

6. Organizations Focused on Advocacy and Education

• Recommended Software: Blackbaud Financial Edge NXT
• Why? This software offers powerful tools for managing complex funding streams and provides strong support for creating detailed impact reports that appeal to donors and grant providers.

Additional Tips for Choosing Software

• Trial Periods: Take advantage of free trials or demos to ensure the software meets your organization’s specific needs.
• Customization Needs: If your nonprofit has unique accounting needs, consider platforms that offer custom reports and dashboards.
• Budget Considerations: Always check for nonprofit discounts or grant opportunities to reduce software costs.

Insider Tips From Experienced Managers

Experienced nonprofit managers look beyond standard feature lists and focus on real-world functionality, efficiency, and alignment with organizational goals. Here are key considerations that experienced managers prioritize:

1. True Fund Accounting Capabilities

• Separation of Funds: Managers understand the importance of maintaining clear distinctions between restricted and unrestricted funds. They look for software that automatically categorizes funds based on donor restrictions or grant requirements.
• Tracking Multiple Programs: Nonprofits often run several programs simultaneously. The software must allow tracking of income and expenses per project or program, which is crucial for transparency and accountability.
• Allocating Expenses: Advanced users seek systems that can allocate shared expenses (e.g., rent, utilities) across multiple programs accurately.

2. Robust Reporting and Compliance Tools

• Grant and Donor Reporting: Managers know that creating customized reports for grants and donor communications can save significant time. They look for software that can generate these reports with minimal manual adjustments.
• Compliance Support: Experienced managers ensure the software helps maintain compliance with accounting standards like FASB and IRS requirements, particularly for generating IRS Form 990.
• Audit Preparation: They prefer tools that provide detailed audit trails and can simplify the audit process by organizing and providing easy access to necessary financial records.

3. User Access Controls and Permissions

• Role-Based Access: Managers understand the need for different access levels to protect sensitive financial data. They choose software that allows customizable permissions, ensuring staff only access the data they need.
• Security Features: Experienced managers prioritize software with robust security measures, including encryption, multi-factor authentication, and secure backups.

4. Integration with Other Systems

• CRM and Fundraising Platforms: Nonprofits often use specialized donor management systems like Salesforce or Bloomerang. Experienced managers look for accounting software that integrates seamlessly with these tools to avoid manual data entry.
• Payment Processors: Nonprofits accepting online donations need smooth integration with platforms like PayPal, Stripe, or dedicated nonprofit fundraising tools.
• Project Management Tools: For organizations managing grants or projects, integration with tools like Asana or Trello can streamline expense tracking and budgeting.

5. Scalability and Flexibility

• Growth Considerations: Managers with long-term experience choose software that can grow with the organization. This includes accommodating more users, handling additional financial complexity, and offering advanced features as needed.
• Modular Features: They appreciate software that allows purchasing additional modules over time, avoiding the need for costly software changes as the nonprofit expands.

6. Support and Training Resources

• Vendor Support: Experienced managers know that reliable, knowledgeable customer support can make a significant difference, especially during onboarding or when troubleshooting issues.
• Training Tools: They value software that offers robust training materials, including tutorials, webinars, and a responsive help center, which helps staff get up to speed quickly.

7. Cost Management and Budgeting Tools

• Budgeting Features: Managers with financial expertise look for advanced budgeting tools that support multiple scenarios, helping nonprofits prepare for variable funding situations.
• Expense Management: They prefer software that offers expense tracking, approval workflows, and real-time budget vs. actuals comparisons to avoid overspending.

8. Value for Money

• Nonprofit Discounts: Experienced managers are often aware of discounts and grants available to nonprofits for purchasing accounting software. They evaluate whether the software provides good value relative to its cost.
• Avoiding Hidden Fees: They scrutinize contracts for hidden costs, such as fees for additional users, data storage, or premium support services.

Pro Tip:

Managers who have worked with multiple systems often test how well the software handles unusual accounting scenarios specific to nonprofits, such as in-kind donations, volunteer hour tracking, and multi-year pledges.

Why Nonprofits Need Specialized Accounting Software

Unique Financial Needs of Nonprofits

Nonprofits operate differently from for-profit businesses, with unique financial management needs that require specialized tools. Unlike traditional businesses focused on profitability, nonprofits must prioritize transparency, accountability, and effective resource allocation. This distinction leads to several specific accounting needs:

Fund Accounting

Nonprofits often receive funds with specific restrictions, such as grants or donations earmarked for particular programs. Fund accounting allows organizations to separate restricted and unrestricted funds, ensuring compliance with donor requirements and providing clear financial statements.

Grant and Donation Tracking

Nonprofits rely on grants, donations, and fundraising events for funding. Accounting software designed for nonprofits offers features to track pledges, manage recurring donations, and monitor grant requirements, helping maintain accurate records and build trust with stakeholders.

Program-Based Budgeting

Nonprofits need to allocate budgets not only for operational costs but also for specific programs and projects. Specialized software enables detailed tracking of income and expenses by program, supporting better financial planning and reporting.

Compliance and Reporting

Nonprofits are held to high standards of financial transparency by regulatory bodies and stakeholders. Accounting software tailored for nonprofits offers built-in reporting templates that comply with standards such as GAAP (Generally Accepted Accounting Principles) and FASB (Financial Accounting Standards Board) guidelines.

Benefits of Using Nonprofit Accounting Software

Enhanced Financial Transparency

By providing detailed insights into how funds are used, specialized software helps nonprofits maintain transparency. Many solutions offer real-time dashboards, customizable reports, and automated financial statements, allowing organizations to present clear financial data to boards, donors, and regulatory agencies.

Streamlined Donation and Grant Management

Software with built-in tools for tracking donations and managing grants can automate many administrative tasks. Features like donor management systems and grant tracking modules reduce manual data entry, minimize errors, and improve fundraising efficiency.

Simplified Budget Management

Nonprofit accounting software often includes advanced budgeting tools that allow organizations to create, monitor, and adjust budgets with ease. Many platforms also support scenario planning and financial forecasting, helping nonprofits prepare for changes in funding or expenses.

Automated Compliance Tracking

Compliance is critical for maintaining nonprofit status and avoiding legal issues. Many accounting solutions provide automated alerts and pre-built templates for compliance reporting, ensuring that organizations meet all legal and regulatory requirements without added stress.

Understanding Compliance Requirements for Nonprofits

Key Compliance Standards for Nonprofits

Nonprofits must adhere to specific accounting and reporting standards to maintain their tax-exempt status and build trust with donors and stakeholders. The most common compliance frameworks include:

1. GAAP (Generally Accepted Accounting Principles)

• Nonprofits must follow GAAP guidelines for financial reporting, ensuring accuracy and consistency in financial statements.
• GAAP standards help create transparent reports that are understandable to donors, board members, and regulatory bodies.

2. FASB (Financial Accounting Standards Board) Guidelines

• The FASB issues specific accounting standards for nonprofits, including guidance on revenue recognition, lease accounting, and reporting requirements.
• FASB ASC 958 is particularly important for nonprofits, as it addresses financial statements and disclosure requirements.

3. IRS Requirements for 501(c)(3) Organizations

• Nonprofits with 501(c)(3) status must file annual Form 990, detailing financial activities, fundraising efforts, and compliance with operational requirements.
• Accounting software with nonprofit-specific features can automate Form 990 preparation, reducing errors and saving time.

4. Grant Compliance

• Many grants, especially from government sources, come with strict reporting requirements.
• Nonprofit accounting software helps track grant funds separately, ensuring that spending aligns with grant conditions and aiding in accurate reporting to grant providers.

Consequences of Noncompliance

• Loss of tax-exempt status, which can lead to significant financial strain.
• Reduced donor trust and potential loss of funding.
• Legal penalties and damage to the organization’s reputation.

How Nonprofit Accounting Software Assists with Compliance

• Built-in templates for financial reports that meet regulatory standards.
• Automated reminders for filing deadlines, such as Form 990 submissions.
• Features for segregating restricted and unrestricted funds, helping maintain clear and compliant financial records.

Final Thoughts

Choosing the best accounting software for your nonprofit is a critical decision that can significantly impact your organization’s financial health, compliance, and operational efficiency. The right software not only helps manage day-to-day finances but also ensures transparency, simplifies compliance with regulatory requirements, and supports strategic decision-making.

When selecting a solution, consider your nonprofit’s specific needs—whether it’s robust fund accounting, grant management, donor tracking, or advanced reporting features. Small nonprofits and startups might find QuickBooks Nonprofit or Aplos Accounting to be cost-effective and user-friendly choices. Mid-sized organizations needing more advanced features may benefit from Sage Intacct Nonprofit, while large nonprofits with complex accounting needs might prefer the powerful tools of Blackbaud Financial Edge NXT or Nonprofit+.

Experienced nonprofit managers know to look beyond just features, focusing on software that offers scalability, ease of use, and strong support. They also consider the importance of integration with existing systems and the software’s ability to grow with the organization.

By carefully evaluating the software against your nonprofit’s goals, budget, and operational requirements, you can find a solution that not only keeps your finances in check but also empowers your organization to focus on its mission and maximize its impact. If you’re ready to take the next step, start by exploring free trials, watching demos, and involving key stakeholders in the decision-making process. With the right accounting software, your nonprofit will be better equipped to thrive and drive positive change.