Many of the forms used by organizations with tax exempt status must be filed electronically, and some also require payment of a user fee. This can be confusing because there are multiple e-filing platforms and some of the rules regarding e-filing recently changed. This page highlights some of the typical filing requirements of 501(c) organizations, with a focus on electronic filing.

If you are starting a 501(c)(3) organization, you generally must submit a Form 1023, Application for Recognition of Exemption Under Section 501(c)(3) of the Internal Revenue Code, or the streamlined version, Form 1023-EZ. For other types of § 501(c) organizations, you generally may seek recognition of tax-exempt status using:

• Form 1024, Application for Recognition of Exemption Under Section 501(a) or Section 521 of the Internal Revenue Code series, or
• Form 1024-A, Application for Recognition of Exemption Under Section 501(c)(4) of the Internal Revenue Code.

All of these forms must be filed electronically via Pay.gov, and you must include payment of a user fee. The fees are updated annually.

Separately, if you are starting a 501(c)(4) organization, you must submit a Form 8976, Notice of Intent to Operate Under Section 501(c)(4), within 60 days of the organization being established. You must submit the form electronically using the IRS Online Registration System and pay a $50 fee. No special software is needed; you just need an email address to activate a login id and password.

Most exempt organizations must file an annual information return known as the Form 990, Return of Organization Exempt from Income Tax, or the streamlined version, Form 990-EZ. The return is generally due by the 15th day of the 5th month after the close of the organization’s tax year. The return must be filed electronically. Organizations can file the form using an IRS Authorized e-File Provider.

Small organizations can meet the requirement by filing the Form 990-N (e-Postcard). The Form 990-N is filed directly with the IRS, and the filer must have an account with Login.gov or ID.me.

Despite their name, there are times when tax-exempt organizations must file tax returns and pay tax.

• An organization with unrelated trade or business income of at least $1,000 must file a Form 990-T, Exempt Organization Business Income Tax Return. The return is generally due by the 15th day of the 5th month after the end of the organization’s tax year. Also, an organization must pay quarterly estimated tax if it expects to owe at least $500 in tax during the year.
• Organizations must pay any applicable excise taxes, including a variety of special excise taxes that are reported on the Form 4720, Return of Certain Excise Taxes on Charities and Other Persons Under Chapters 41 and 42 of the Internal Revenue Code.

The Form 990-T must be filed electronically. The Form 4720 must be e-filed by private foundations and, beginning with tax years ending on or after December 30, 2023, by anyone who files at least ten returns in a calendar year. Organizations can file these returns electronically through an IRS Authorized e-File Provider. Tax payments must be made electronically, such as by using the Electronic Federal Tax Payment System.

Exempt organizations with employees must file employment tax returns and pay employment taxes. These returns may be filed electronically. For more information, see Employment Taxes for Exempt Organizations and Electronic Filing and Payment Options for Employment Tax Returns of Exempt Organizations.

Exempt organizations may be required to file information returns (Form 1099 series) to report certain payments. For example, an organization must file the Form 1099-NEC, Nonemployee Compensation, to report payments made to an independent contractor if the payments exceed at least $600 during the year. The deadlines vary by return. The returns generally must be filed electronically using the Information Return Intake System if the organization files at least ten information returns during the year.

In limited situations, you may need to file the Form 8940, Request for Miscellaneous Determination, to ask the IRS to make certain determinations about the organization and its activities. You must submit the form electronically using Pay.gov and pay a user fee. The fee is adjusted annually and varies by the type of determination (for the 2024 fees, see Appendix A of Rev. Proc. 2024-5).

You can use Form 8868, Application for Extension of Time To File an Exempt Organization Return or Excise Taxes Related to Employee Benefit Plans, to apply for an automatic extension of certain exempt organization returns, including Forms 990, 990-T, and 4720. The Form 8868 may be filed electronically. For more information, see Instructions for Form 8868, Application for Extension of Time To File an Exempt Organization Return or Excise Taxes Related to Employee Benefit Plans.

The Taxpayer Advocate Service is an independent organization within the IRS. TAS helps taxpayers resolve problems with the IRS, makes administrative and legislative recommendations to prevent or correct the problems, and protects taxpayer rights. TAS helps all taxpayers (and their representatives), including individuals, businesses, and exempt organizations. You may be eligible for free TAS help if your IRS problem is causing financial difficulty, if you’ve tried and been unable to resolve your issue with the IRS, or if you believe an IRS system, process, or procedure just isn’t working as it should.

TAS has offices in every state, the District of Columbia, and Puerto Rico. To find your local advocate’s number:
• Visit www.TaxpayerAdvocate.irs.gov/contact-us;
• Check your local directory; or
• Call TAS toll-free at 877-777-4778.

Low Income Taxpayer Clinics (LITCs) assist individuals whose income is below a certain level who need to resolve tax problems with the IRS. They also provide education, outreach, and information on taxpayer rights to individuals who speak English as a second language. LITCs represent taxpayers in disputes before the IRS and courts and help taxpayers respond to IRS notices and correct account problems. Services are offered for free or a small fee. LITCs are independent from the IRS and TAS. For more information or to find an LITC near you, see the LITC Page or Publication 4134, Low Income Taxpayer Clinic List. You can also request Pub. 4134 by calling 800-TAX-FORM (800-829-3676).