Top 10 Best Nonprofit Bookkeeping Software of 2026

Aplos is a cloud-based accounting software tailored specifically for nonprofits, churches, and mission organizations, offering fund accounting to track restricted and unrestricted funds seamlessly. It handles donation management, pledge tracking, budgeting, expense allocation, and compliance reporting like Form 990 preparation. The platform integrates with online giving tools and payment processors for streamlined revenue tracking and automated bank reconciliations.

QuickBooks Online Nonprofit is a cloud-based accounting solution from Intuit, customized for nonprofits with features like class and location tracking for fund accounting, donation and grant management, and compliance reporting. It handles core bookkeeping tasks such as invoicing, expense tracking, payroll integration, and financial statements tailored to nonprofit needs like Form 990 support. Ideal for organizations seeking scalable, familiar software without fully specialized nonprofit ERP systems.

Sage Intacct is a robust cloud-based financial management platform designed for nonprofits, providing advanced fund accounting, grant tracking, and multi-entity management to handle complex financial structures. It offers real-time reporting, automated workflows, and compliance tools tailored to nonprofit needs like donor-restricted funds and program budgeting. Ideal for scaling organizations, it integrates seamlessly with CRM systems and supports customizable dashboards for better financial oversight.

Blackbaud Financial Edge NXT is a cloud-based accounting platform tailored for nonprofits, providing fund accounting, general ledger management, budgeting, and financial reporting. It supports complex nonprofit structures with features like grant tracking, multi-entity consolidation, and compliance with standards such as FASB and GASB. The software integrates deeply with Blackbaud's ecosystem, including Raiser's Edge NXT for fundraising, enabling streamlined operations across finance and donor management.

MIP Fund Accounting, offered by Community Brands, is a robust fund accounting software tailored for nonprofits, government agencies, and public sector organizations. It excels in managing complex fund structures, grant tracking, budgeting, and financial reporting compliant with nonprofit GAAP and FASB standards. The platform supports multi-entity consolidation, automated workflows, and customizable dashboards to streamline nonprofit financial operations.

FastFund by Araize is a cloud-based nonprofit accounting software focused on fund accounting, enabling organizations to manage multiple funds, grants, and budgets with precision. It provides tools for financial reporting, donor tracking, and compliance with nonprofit standards like FASB. The platform integrates with payroll and banking systems, streamlining operations for small to mid-sized nonprofits.

Denali Fund by Cougar Mountain Software is a robust, nonprofit-specific accounting solution offering fund accounting, donor management, grant tracking, and compliance tools tailored for 501(c)(3) organizations. It supports unlimited funds, encumbrance accounting, budgeting, and customizable reporting to handle complex nonprofit finances. Ideal for organizations needing detailed tracking of restricted and unrestricted funds while maintaining FASB and GAAP compliance.

NetSuite for Nonprofits is a cloud-based ERP platform from Oracle, specifically adapted for nonprofit organizations with robust bookkeeping, fund accounting, and financial management capabilities. It excels in tracking grants, managing donor relationships, and ensuring compliance with standards like FASB and GAAP through multi-entity and multi-book accounting. The solution integrates seamlessly with CRM, inventory, and project management modules for a holistic operational view.

Xero for Nonprofits is a cloud-based accounting software adapted for nonprofit organizations, offering tools for tracking donations, grants, expenses, and multiple funds through tracking categories and custom reports. It automates bank reconciliations, invoicing, and payroll while integrating with donor management apps like Bloomerang and Kindful. Ideal for nonprofits needing scalable bookkeeping without heavy customization, it provides real-time financial visibility and multi-user collaboration.

Wave Accounting is a cloud-based platform offering free invoicing, accounting, and receipt scanning for small businesses and organizations. For nonprofits, it provides basic bookkeeping tools like income/expense tracking, bank reconciliation, and simple financial reports. However, it lacks specialized nonprofit features such as fund accounting, donor management, or Form 990 support, making it best for very small operations with straightforward finances.