Top 10 Best Nonprofit Tax Software of 2026

Tax990 is a cloud-based software platform specializing in nonprofit tax preparation and e-filing for IRS Forms 990, 990-EZ, 990-N, 990-PF, and related schedules, along with state charitable registrations. It provides step-by-step guided interviews, automatic calculations, compliance checks, and professional review options to ensure accuracy and IRS acceptance. Designed for nonprofits of all sizes, it streamlines the entire process from data entry to electronic submission and receipt tracking.

ExpressTaxExempt is a cloud-based platform specialized for tax-exempt organizations to prepare and e-file IRS Form 990 series returns, including 990, 990-EZ, 990-N, and associated schedules. It features a guided interview process, data import from prior years or Excel, and direct electronic submission to the IRS with real-time status updates. The software emphasizes accuracy with built-in validations and offers unlimited amendments for filed returns.

File990 (file990.org) is a free online platform designed specifically for nonprofits to prepare and e-file IRS Form 990 series returns, including 990, 990-EZ, 990-N, and select state forms. It guides users through a step-by-step interview process to ensure compliance without needing tax expertise. The tool emphasizes simplicity and accessibility, making annual tax filings efficient for smaller organizations.

Aplos is a cloud-based accounting software tailored for nonprofits, providing fund accounting, donation management, and tools for preparing and e-filing Form 990 series tax returns. It integrates everyday bookkeeping with tax compliance, allowing organizations to track restricted funds and generate necessary schedules directly from financial data. The platform emphasizes ease of use for non-accountants while ensuring IRS-compliant reporting.

QuickBooks Online Nonprofit is a cloud-based accounting platform tailored for nonprofits, providing fund accounting, donor management, and customizable reporting to support financial transparency required for tax compliance like Form 990. It excels in tracking donations, grants, and expenses by program or fund using class and location tracking, generating statements that feed into tax preparation. While not a dedicated tax filing tool, it organizes data efficiently for accountants or export to specialized 990 software.

Sage Intacct is a cloud-based ERP and financial management platform tailored for nonprofits, providing robust fund accounting, grant tracking, and compliance reporting essential for tax preparation. It excels in generating detailed financial statements and schedules that support Form 990 filing, with multi-dimensional tracking for programs, funds, and grants. While not a dedicated tax filing tool, it streamlines data export to specialized tax software, ensuring GAAP and FASB compliance.

Blackbaud Financial Edge NXT is a cloud-based fund accounting platform tailored for nonprofits, providing comprehensive financial management including general ledger, budgeting, accounts payable/receivable, and grant tracking. It excels in generating detailed financial reports and statements crucial for nonprofit tax compliance, such as supporting Form 990 preparation through customizable dashboards and analytics. While not a dedicated tax filing tool, it streamlines the data aggregation and reporting needed for accurate tax submissions and audits.

MIP Fund Accounting, offered by Community Brands, is a robust cloud-based ERP system tailored for nonprofits, providing fund accounting, budgeting, and financial reporting with built-in support for tax compliance. It excels in tracking restricted funds, grants, and generating essential forms like 990 and 990-EZ directly from the general ledger. While primarily an accounting platform, its tax tools make it suitable for nonprofits handling complex financials alongside tax prep.

Drake Software is a comprehensive professional tax preparation platform that supports nonprofit tax returns, including the full Form 990 series (990, 990-EZ, 990-N, 990-PF, and related schedules). It provides tools for electronic filing, diagnostics, data import/export, and multi-state compliance, making it suitable for tax professionals handling nonprofit clients. The software integrates with practice management features and offers robust error-checking to ensure accurate filings.

UltraTax CS is a professional-grade tax preparation software from Thomson Reuters, tailored for CPAs and accounting firms handling complex returns, including the full suite of nonprofit Forms 990, 990-EZ, 990-PF, and 990-N. It offers robust calculations, state return support, and integration with practice management tools like CS Professional Suite. Ideal for high-volume preparers, it emphasizes accuracy, diagnostics, and electronic filing efficiency for nonprofit organizations.