TL;DR: The most reliable accounting software for nonprofits in 2026 includes QuickBooks Online, Sage Intacct, Aplos, and other fund-accounting tools built for grant tracking and compliance. Each excels in different areas depending on budget and complexity. This guide compares the top 6 picks on features, pricing, and nonprofit-specific capabilities.
Managing your nonprofit’s finances isn’t easy. First, you need to stay compliant with the Internal Revenue Service (IRS) while keeping track of grants, donations, and program costs. Add in the complexity of filing tax forms such as Form 990, and it becomes clear why the right accounting software is essential for nonprofits aiming to maintain tax-exempt status and meet particular reporting requirements. Properly managed accounting data is the foundation for making informed decisions and maintaining your organization’s financial health. Nonprofit-specific features, such as fund tracking and donation management, are crucial in accounting software to address the unique needs of nonprofit organizations. A financial management solution tailored for nonprofits can address these needs by providing comprehensive tools for fund accounting, regulatory compliance, real-time reporting, and automating routine financial tasks. In addition to IRS compliance, nonprofits must also adhere to standards set by the Financial Accounting Standards Board (FASB), which ensures transparency and consistency in nonprofit financial reporting, including the preparation of standard financial reports like the Balance Sheet and Profit and Loss statement.
- Introduction to Nonprofit Accounting
- Key Features of Accounting Software for Nonprofits
- Streamline nonprofit finances with these best-in-class tax and accounting tools
- Accept donations and payment processing: Essential tools for modern nonprofits
- Donor management: Why it matters and how top software helps
- Which version of the Form 990 should nonprofits file?
- Why nonprofit accounting software matters
- Ready to simplify your nonprofit's tax filing and accounting?
To simplify your search and help you find the six best accounting software options for nonprofits in 2025. When evaluating these options, consider key features like grant management, donor tracking, and compliance reporting, which are essential for nonprofit operations. Look for the ability to link your bank account for easier transaction management and bank reconciliation, as well as tracking tools to monitor expenses, donations, and grants. Straightforward accounting software can simplify financial management for nonprofits and small businesses alike. The most reliable accounting software options for nonprofits in 2025 include QuickBooks Nonprofit, Sage Intacct, Xero, Blackbaud Financial Edge NXT, and Aplos. Some solutions are better suited for large nonprofits due to their scalability and ability to handle complex operations, while others are ideal for smaller nonprofits because of their low cost and ease of use. It’s important to find accounting software tailored to the unique requirements of nonprofits to ensure usability, affordability, and regulatory compliance. For smaller nonprofits, low cost is especially important to help manage limited budgets while maintaining compliance and efficiency.
Introduction to Nonprofit Accounting
Nonprofit accounting serves as your organization’s financial compass, guiding mission-driven teams through complex waters that go far beyond basic bookkeeping. This specialized discipline empowers you to navigate fund accounting, master financial stewardship, and maintain the compliance that protects your donor relationships. Unlike for-profit enterprises, nonprofits sail through unique financial currents—tracking restricted and unrestricted funds, stewarding grants with precision, and ensuring transparent reporting that builds stakeholder trust. Some organizations may rely on an in-house accountant to manage these complexities, but this can be costly and time-consuming. Many nonprofits benefit from outsourcing their accounting functions to external firms to access expertise at a lower cost. Most accounting software for nonprofits is built with for-profits in mind, making it essential to find solutions that cater specifically to nonprofit needs. Your accountability to donors, grantmakers, and regulatory bodies makes accurate and timely financial reporting not just essential, but mission-critical.
The right nonprofit accounting software transforms these challenges into opportunities, equipping your team with powerful tools that streamline fund accounting, simplify grant management, and strengthen donor relationships. Many organizations have complex accounting needs that require more advanced solutions than basic software can provide. Mission-aligned accounting solutions empower organizations to generate comprehensive financial reports that satisfy both internal leadership and external stakeholders with confidence and clarity. An intuitive platform becomes your crew’s trusted navigator, enabling staff and volunteers to efficiently manage accounting tasks without steep learning curves that drain precious time from your core mission.
Cloud-based solutions chart the course for modern nonprofit financial management, delivering real-time access to critical data while fostering seamless collaboration and enterprise-level security that protects donor trust. Cloud-based nonprofit accounting software is generally considered secure due to robust security features such as data encryption and user access controls. Smart integration capabilities multiply your impact by connecting fundraising platforms, payroll systems, and essential operational tools into one cohesive ecosystem that streamlines your entire financial workflow. When nonprofits choose the right accounting software, they don’t just overcome financial challenges—they transform technology into a vessel for greater mission impact, maintain unwavering compliance, and free their teams to focus on the work that matters most.
Key Features of Accounting Software for Nonprofits
When choosing accounting software that truly serves your nonprofit’s mission, focus on features that understand your unique challenges and empower your impact. The cornerstone capability you need is robust fund accounting – this isn’t just bookkeeping, it’s your shield for maintaining donor trust and regulatory compliance. Nonprofit accounting software should allow for scalability to accommodate the varying needs of small versus large organizations. The right system protects both restricted and unrestricted funds, ensuring every dollar flows exactly where donors intended and grantors required. This transparency becomes your foundation for building unshakeable stakeholder confidence.
Your organization deserves reporting tools that tell your impact story clearly and compellingly. Customizable reporting is essential for nonprofits to meet specific stakeholder needs and adapt to changing requirements. Effective accounting software transforms complex financial data into powerful narratives – generating crisp financial statements, intuitive cash flow dashboards with data visualizations, and comprehensive grant reports and annual reports that showcase your financial stewardship. Nonprofit organizations often need to create custom reports and custom reports for different funds or purposes to communicate their financial position to stakeholders. The best nonprofit accounting software allows users to customize reports and generate specialized reports for regulatory or board requirements. When board members, donors, and program managers can instantly grasp your financial health, you’re empowering informed decisions that amplify your mission reach.
Smart expense tracking and donation management shouldn’t feel like administrative burden – they should streamline your operations and free your team to focus on what matters most. Look for solutions that make monitoring spending effortless while accurately capturing every contribution, turning financial management from a necessary evil into a mission multiplier. Your staff and volunteers deserve tools that work as hard as they do for your cause.
Integration capabilities become your operational superpower, connecting accounting seamlessly with payroll, fundraising platforms, and other mission-critical systems. Combined with an intuitive interface that welcomes rather than intimidates users, these features transform technology from obstacle to accelerator. Solutions like QuickBooks Online, Blackbaud Financial Edge NXT, Xero, and Zoho Books offer these empowering capabilities, helping you channel more resources toward impact rather than administrative complexity. When you choose accounting software that truly understands nonprofit needs, you’re not just improving financial management – you’re protecting donor trust, enhancing transparency, and making strategic decisions that propel your mission forward.
Streamline nonprofit finances with these best-in-class tax and accounting tools
The following tools simplify data entry, offer robust reporting features—including core accounting features such as expense tracking, donation processing, and compliance reporting—support fund accounting, and streamline e-file capabilities for forms such as Form 990-N, 990-EZ, and 990-PF, while also providing collaboration tools that facilitate teamwork and real-time data sharing among nonprofit staff. Many solutions also include project management, project accounting for tracking project-related financials and grants, and inventory management functionalities, allowing organizations to track projects and manage product inventories within their financial workflows. Advanced features like financial forecasting help with planning and budgeting, giving nonprofits better insight into their future financial health. Integration capabilities often extend to fundraising software and nonprofit fundraising platforms, ensuring seamless data flow between accounting, donor management, and fundraising systems. These tools support key activities such as managing fundraising campaigns and event registration, making them especially valuable for nonprofits and churches. They can generate comprehensive accounting reports required for nonprofit compliance and help automate and simplify various accounting tasks, from payroll to project costing. Additionally, these solutions can automate tasks related to fundraising and financial management, streamlining operations and improving efficiency so staff can focus more on relationship-building activities.
QuickBooks Nonprofit: Best overall tax software for nonprofits
QuickBooks has established itself as a trusted leader in small business accounting, and its nonprofit version continues to uphold that reputation. The latter offers specialized features for tax-exempt organizations, including tracking donor contributions, managing grants, and preparing IRS-compliant reports. QuickBooks allows you to categorize revenue expenditures by fund or program. QuickBooks is trusted by many nonprofits for its reliability and widespread adoption in the sector.
With QuickBooks Nonprofit, you can enjoy benefits such as:
A dedicated fund accounting structure, including the ability to track individual funds for more granular reporting and management
Streamlined accounts payable management
Integrated payroll management
Simple integration with donation platforms
Templates for Form 990 and other tax forms
Electronic file management with QuickBooks Online add-ons
Easy tracking of public support, unrelated business taxable income, and expenses
Linking your bank account for seamless transaction reconciliation
Bank reconciliation to ensure your records match your bank statements
Double entry accounting for accurate financial management
Ability to generate standard financial reports such as Balance Sheet and Profit and Loss statements
Built-in tracking tools for monitoring expenses, donations, and grants
When considering QuickBooks Nonprofit, it’s important to review the monthly price structure and ensure you understand all costs before committing, as pricing transparency can vary among accounting software providers.
Why you’ll love it: QuickBooks streamlines the process for both internal bookkeeping and IRS form preparation, helping you stay compliant with federal and state reporting requirements. |
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Why you’ll love it: QuickBooks streamlines the process for both internal bookkeeping and IRS form preparation, helping you stay compliant with federal and state reporting requirements.
Why you’ll love it: QuickBooks streamlines the process for both internal bookkeeping and IRS form preparation, helping you stay compliant with federal and state reporting requirements.
Aplos: Simplest for IRS-compliant reporting and Form 990
Aplos is accounting software designed specifically for nonprofit organizations and religious institutions. If you want a system that automates fund accounting while also managing donor communications and event registrations, Aplos is worth considering. Aplos offers true fund accounting, integrated donor management, compliance support, and tools for online donations and events.
Here are the features that make the software stand out:
Built-in support for Form 990, Form 990-N, and state return
Smart donation tracking and automated thank-you notes
Integration with multiple bank accounts for streamlined reconciliation and easy management of bank account information
Nonprofit reporting tools for tracking donations, grants, and ensuring regulatory compliance
Built-in tracking tools for monitoring financial activities and donor engagement
Ability to manage donor information for better engagement, donation tracking, and compliance
Tag donations to categorize financial transactions for more accurate tracking, fund-specific reporting, and streamlined financial oversight
Calendar year and fiscal year tracking for annual form filings
User-friendly interface for quick data entry
Comprehensive support for fund accounting nonprofits, including management of restricted and unrestricted funds
Robust donor reporting capabilities for effective management of donations, grants, and compliance
Why you’ll love it: Aplos is ideal for those who want to prepare and submit IRS forms without needing a background in accounting or tax law. |
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Why you’ll love it: Aplos is ideal for those who want to prepare and submit IRS forms without needing a background in accounting or tax law.
Why you’ll love it: Aplos is ideal for those who want to prepare and submit IRS forms without needing a background in accounting or tax law.
Sage Intacct: Best for midsize to large exempt organizations
Sage Intacct is a cloud-based accounting platform tailored for complex organizations with advanced financial management needs, delivering advanced financial capabilities that suit larger exempt organizations, private foundations, and political organizations. It offers multi-entity consolidation, audit trails, and powerful dashboards for effective financial management. Sage has over 30 years of experience serving nonprofits and has empowered thousands of organizations. Sage offers specialized nonprofit and fund accounting solutions through Sage Intacct, including features, discounts, and integrations designed to address fund management, compliance, and automation needs.
It also empowers your organization to:
Handle long-form filings and Form 990-PF
Generate comprehensive income tax return reports
Leverage built-in custom workflows for approvals and budgeting
Track income, expenses, and taxes across multiple programs
Optimize resource allocation across programs and initiatives with dedicated tools
Use analytics and dashboards to monitor the organization’s financial health
Access financial forecasting tools for planning and budgeting
Utilize double entry accounting for precise financial tracking
Generate standard financial reports for compliance and analysis
Generate comprehensive financial statements for compliance and transparency
Meet Internal Revenue Code standards
Manage fixed assets throughout their lifecycle, from acquisition to disposal
Why you’ll love it: For nonprofits with complex needs, Sage Intacct makes compliance, internal management, and financial strategy much easier. |
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Why you’ll love it: For nonprofits with complex needs, Sage Intacct makes compliance, internal management, and financial strategy much easier.
Why you’ll love it: For nonprofits with complex needs, Sage Intacct makes compliance, internal management, and financial strategy much easier.
Zoho Books: Best for small nonprofits looking to reduce costs
Known for its affordability and robust features, Zoho Books is great for nonprofits and small businesses that need basic account tracking and want to avoid bloated software. Zoho Books is also available as free accounting software for small nonprofits, making it an accessible choice for organizations with limited budgets. Zoho Books offers a truly free plan for any organization and provides a 15% discount for most nonprofits.
Its simple yet powerful features include:
Straightforward accounting software with a user-friendly interface
Automated workflows for tax filing and reports
Easy tracking of grants, income, and expenses
Robust tracking expenses features to help categorize expenditures and maintain budget control
Bank integration with the ability to link your bank account for real-time transaction updates
Bank reconciliation features for accurate record-keeping and matching your bank statements with your financial records
Inventory management tools for tracking stock and managing product inventories
Mobile app for accounting on the go
Custom chart of accounts to match fund accounting principles
Free nonprofit accounting software option for organizations with limited budgets
Cloud based accounting software solution for real-time access and remote collaboration
Free version available for organizations with limited needs
Why you'll love it: Zoho helps you reduce costs while keeping your organization compliant and organized. It's ideal for nonprofits that are just getting started or operating on limited budgets. |
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Why you’ll love it: Zoho helps you reduce costs while keeping your organization compliant and organized. It’s ideal for nonprofits that are just getting started or operating on limited budgets.
Why you’ll love it: Zoho helps you reduce costs while keeping your organization compliant and organized. It’s ideal for nonprofits that are just getting started or operating on limited budgets.
Nonprofit+: Full-featured nonprofit suite including extension form support
Built on the Acumatica xRP Platform, Nonprofit+ is one of the leading nonprofit accounting solutions, offering everything from fund accounting to donor CRM and grant management. It’s especially useful for nonprofits needing advanced features such as automatic extension filings and audit prep.
Nonprofit+ excels in the following areas:
Managing grants and funds life cycle
Real-time financial reporting tailored to IRS needs
Handling of extension form requests and filing workflows
Compliance tracking for Form 990, Form 990-EZ, and Form 990-PF
Tracking of donations, unrelated business taxable income, and overhead
Comprehensive accounting solutions for nonprofits
Managing restricted funds and ensuring compliance with donor restrictions
Tracking restricted funds for grants and donations
Project management features for coordinating programs and initiatives
Built-in tracking tools for monitoring financial activities and donor engagement
Integration with nonprofit fundraising platforms for streamlined donation management
Tools for managing fundraising campaigns and tracking their success
Event registration features for organizing and managing events
|Why you’ll love it: Nonprofit+ is a comprehensive platform, making it the perfect fit for organizations that want all-in-one control over compliance, grants, and program finances. Implementation costs should be considered when adopting a full-featured platform like Nonprofit+.|
Blackbaud Financial Edge NXT: Best for complex grants and reporting
Blackbaud is a trusted name in nonprofit tech, and Financial Edge NXT provides a powerful platform for complex accounting and compliance. Its strengths lie in form preparation and multiple form handling, including state return and California form requirements.
Moreover, Financial Edge NXT makes financial management easier by:
Providing deep reporting tools for federal income taxes and Form 990 filing
Tracking public support to maintain tax-exempt status
Collaborating with tax professionals for review and accuracy
Being compatible with the IRS e-file system
Simplifying the request and tracking of automatic extensions
Offering integrated membership management tools for tracking member data and engagement
Supporting global nonprofits with multi-currency management and international compliance features
Including advanced cash management features to automate financial processes and improve reporting
Featuring nonprofit reporting tools for tracking grants, donations, and compliance
Offering built-in tracking tools for monitoring financial activities and donor engagement
Allowing management of multiple bank accounts for streamlined financial operations
Providing bank reconciliation features for accurate record-keeping
Supporting double entry accounting for precise financial management
Generating standard financial reports for compliance and analysis
Including financial forecasting tools for planning and budgeting
Why you'll love it: If your nonprofit manages several grant sources and needs help juggling multiple reporting timelines, this software gives you precision and peace of mind. |
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Why you’ll love it: If your nonprofit manages several grant sources and needs help juggling multiple reporting timelines, this software gives you precision and peace of mind.
Why you’ll love it: If your nonprofit manages several grant sources and needs help juggling multiple reporting timelines, this software gives you precision and peace of mind.
Accept donations and payment processing: Essential tools for modern nonprofits
For mission-driven organizations, streamlined donation acceptance isn’t just about convenience—it’s about empowering your team to focus on what truly matters: advancing your cause. Modern nonprofit accounting solutions serve as trusted navigators through financial complexity, offering integrated donation and payment tools that transform every supporter interaction into a seamless journey toward impact.
The right accounting platform empowers nonprofits to accept online gifts, manage recurring donations, and process payments from multiple sources—all within one secure, mission-aligned system. These solutions automatically capture and allocate every contribution, ensuring your financial stewardship remains transparent and accurate. This integration doesn’t just streamline operations; it frees your team from manual data entry and reduces errors, allowing you to redirect precious time and resources toward program delivery and community impact.
Purpose-built nonprofit accounting platforms deliver customizable donation forms, automated donor receipts, and real-time insights into giving patterns. These features strengthen supporter relationships by making contributions effortless while providing timely acknowledgments that reinforce donor trust. Integrated payment processing also safeguards your organization through detailed compliance records, helping you navigate audits and regulatory requirements with confidence and peace of mind.
By embracing accounting solutions with built-in donation and payment capabilities, nonprofits can stabilize cash flow, maintain precise financial oversight, and uncover valuable patterns in supporter behavior. This positions organizations to make strategic decisions, optimize outreach efforts, and demonstrate unwavering transparency to donors and stakeholders. Ultimately, these tools serve as essential vessels for any nonprofit committed to operational excellence, robust financial stewardship, and maximizing mission impact.
Donor management: Why it matters and how top software helps
Donor management is at the heart of effective nonprofit accounting, enabling organizations to build lasting relationships with supporters while ensuring every dollar is tracked and reported accurately. For nonprofit organizations, managing donations, grants, and other funding sources isn’t just about recording transactions—it’s about maintaining transparency, accountability, and compliance with regulatory standards. Accurate accounting data is essential for effective donor management and reporting, providing the foundation for informed decision-making and financial oversight.
Top nonprofit accounting software solutions, such as QuickBooks Nonprofit, Aplos, and Blackbaud Financial Edge NXT, are designed with robust donor management tools that streamline the entire process. These platforms allow nonprofits to track donations in real time, manage donor profiles, and generate detailed financial reports that reflect both income and expense tracking. They also support the management of fundraising campaigns, helping organizations track donations and maintain donor relationships to support overall fundraising efforts. For example, QuickBooks Enterprise Nonprofit offers comprehensive donor management features, including tracking donations, managing payroll, and integrating seamlessly with nonprofit fundraising platforms. Aplos stands out with its intuitive donor management tools, making it easy to track giving history, generate thank-you letters, and produce donor-specific financial reports.
Specialized accounting software like ACCOUNTS from Software4Nonprofits and Araize FastFund Accounting address the unique financial challenges faced by nonprofits. These solutions offer advanced fund accounting capabilities, grant management, and tools for managing both restricted and unrestricted funds. Integration with fundraising software is crucial for streamlined operations, ensuring that donor management and fundraising activities are seamlessly connected. This ensures that every donation is allocated correctly, expenses are tracked accurately, and compliance with fund accounting standards is maintained.
When evaluating donor management tools, nonprofits should consider factors such as ease of use, integration capabilities with other systems, and overall cost. The right accounting software for nonprofits will align with your organization’s specific accounting needs, offering advanced features that support donor management, grant tracking, and financial edge reporting. Integration with other donor management tools and nonprofit fundraising platforms can further enhance efficiency, reduce manual data entry, and help maintain compliance with IRS and state requirements. Utilizing tracking tools within these platforms allows nonprofits to monitor donor engagement and fundraising campaign performance, improving oversight and decision-making.
Beyond donor management, leading nonprofit accounting software also supports cash flow management, budget management, and comprehensive financial reporting. These features empower organizations to track expenses, monitor cash flow, and generate reports that provide a clear picture of the nonprofit’s financial position. With accurate financial data at their fingertips, nonprofit leaders can make informed decisions, allocate resources effectively, and demonstrate accountability to donors and stakeholders.
In summary, donor management is a critical component of nonprofit accounting, and choosing the best nonprofit accounting software can make all the difference. By leveraging advanced donor management tools, integrated accounting features, and tracking tools, nonprofits can streamline financial management, maintain compliance, and stay focused on their mission.
Which version of the Form 990 should nonprofits file?
Understanding which version of Form 990 your nonprofit should file is key to staying compliant:
Form 990-N (e-Postcard) – for tax-exempt organizations with gross receipts of $50,000 or less
Form 990 EZ – for organizations with receipts < $200,000 and assets < $500,000
Form 990 (Long Form) – for larger organizations with gross receipts exceeding $200,000 and total assets of $500,000 or more
Form 990 PF – for private foundations
Each version has its own rules, so choosing accounting software that aligns with your form preparation and filing needs is essential. It’s also important to select an accounting tool tailored for nonprofit compliance.
Why nonprofit accounting software matters
Beyond simply tracking dollars in and out, great tax software for nonprofits helps with:
Maintaining tax-exempt status
Avoiding errors in income tax return preparation
Meeting IRS and state reporting requirements
Keeping donor data secure and accurate
Managing grants, funds, and public support thresholds
Simplifying the process of filing forms or requesting an automatic extension
Maintaining accurate financial records for audits, compliance, and transparency
Maintaining accurate accounting data for informed decision-making
Using tracking tools to monitor expenses, donations, and grants
Generating standard financial reports for compliance and transparency
Additionally, nonprofit’s financial management is enhanced when accounting software is integrated with other organizational systems, streamlining financial processes and improving data accuracy.
Ready to simplify your nonprofit's tax filing and accounting?
The right accounting software can transform tax returns into an effortless process. With features such as Form 990 generation, data entry automation, and support for tax-exempt compliance, today’s top software tools enable nonprofits to stay focused on their mission.
If you’re looking for expert guidance, Scottship Solutions is here to help. Our team specializes in supporting nonprofits, exempt organizations, private foundations, and religious institutions with end-to-end form preparation, compliance, and software onboarding.Let us help you simplify your nonprofit’s financial management, reduce costs, and maintain compliance. Get in touch with Scottship Solutions today
Frequently Asked Questions
What makes accounting software for nonprofits different from regular accounting software?
Nonprofit accounting software tracks fund-based accounting, which means separating revenue and expenses by program, grant, or restriction. Regular accounting software focuses on profit and loss. Nonprofits need to track restricted versus unrestricted funds, generate Form 990 reports, manage donor contributions with tax receipts, and report expenses by both function and nature. Standard business tools like basic QuickBooks can work, but you will spend significant time creating workarounds for these nonprofit-specific needs.
How much should a nonprofit budget for accounting software?
Small nonprofits (under $500K annual budget) can find solid options for $0 to $50 per month. QuickBooks Online and Zoho Books both offer affordable plans with nonprofit features. Mid-size organizations typically spend $100 to $500 per month for platforms like Sage Intacct or Blackbaud. The hidden cost is implementation and training: budget $1,000 to $5,000 for initial setup and data migration. Factor in staff time for learning the new system, usually 2 to 4 weeks of reduced productivity.
Can QuickBooks handle nonprofit accounting needs?
QuickBooks works well for small nonprofits, especially with the nonprofit-specific version. It handles basic fund tracking, donor management, and financial reporting. Where it falls short is complex grant management with multiple restrictions, sophisticated allocations across programs, and automated Form 990 preparation. If your organization manages more than 5 to 10 active grants or needs detailed cost allocation, you may outgrow QuickBooks and need a purpose-built nonprofit platform.
What is Form 990 and which software helps prepare it?
Form 990 is the annual information return that most tax-exempt organizations must file with the IRS. It reports your finances, governance, programs, and compensation. Aplos and Nonprofit+ offer built-in Form 990 preparation tools. Other platforms like QuickBooks require you to export data and use a separate tax preparation service. Filing deadlines are 4.5 months after your fiscal year ends, with extensions available. Getting your chart of accounts set up correctly from the start makes 990 preparation significantly easier.
Should a nonprofit use cloud-based or desktop accounting software?
Cloud-based, in almost every case. Cloud platforms give your team access from anywhere, handle automatic backups, and push updates without IT involvement. This matters because nonprofit staff and board members often work remotely or across multiple locations. Desktop software creates version control problems, requires manual backups, and limits who can access financial data. The only scenario where desktop still makes sense is if you have no reliable internet access at your primary work location.