Closing an EIN for a tax exempt organization is described at the IRS website: https://www.irs.gov/businesses/small-businesses-self-employed/canceling-an-ein-closing-your-account
Information for Exempt Organizations
If you applied for an EIN for an exempt organization that:
(1) never applied for formal exemption,
(2) is not covered in a group ruling, or
(3) never filed an information return,
send a letter requesting the closing of your account to:
Internal Revenue Service
Attn: EO Entity
Mail Stop 6273
Ogden, UT 84201
or you may fax it to (801) 620-7116.
State the reason you wish to close your account. If you have a copy of the EIN Assignment Notice that was issued when your EIN was assigned, you should include that when you write. Otherwise, be sure to include the complete legal name of the entity, the EIN, and the mailing address.
Read the 3 criteria listed above carefully. If your organization fits all of the criteria, then write a letter to the IRS and give the reason you are closing your EIN. Usually it is because the organization dissolved or ceased its operations or activities.
If you fail one of the criteria, the IRS has different instructions. https://www.irs.gov/charities-non-profits/termination-of-an-exempt-organization.
You will have to file one more 990-N for the old organization and check “Yes” to the question “Has your organization terminated or gone out of business?” If you typically file the Form 990 or 990-EZ, than check the Terminated box in the header area on page 1.
Additionally, you will need to file a Schedule N, Liquidation, Termination, Dissolution, or Significant Disposition of Assets with your Form 990 or 990-EZ. If you file a 990-N, there is no Schedule N to file.
Carol Topp, CPA