The Taxpayer First Act of 2019 moved exempt organization returns online. For most organizations, a paper Form 990 is no longer an option, and mailing one when e-filing is required doesn't stop the late-filing penalties.
Which returns must be e-filed
| Return | E-filing required |
|---|---|
| Form 990 | Tax years beginning after July 1, 2019 |
| Form 990-PF | Tax years beginning after July 1, 2019 |
| Form 990-EZ | Tax years ending July 31, 2021 and later |
| Form 990-T | Required for organizations and trusts subject to the unrelated business income tax |
| Form 990-N | Always electronic, filed on IRS.gov |
The 2025 instructions for each of these returns repeat the requirement. The one narrow exception for the 990-T is an entity filing it only to make an elective payment election, which may still file on paper. Form 8868, the extension request, can be e-filed as well, though it may still be mailed.
A paper return doesn't count
This is the rule that surprises people. When an organization required to e-file sends a paper return instead, the IRS treats it as having failed to file, "even if a paper return is submitted," in the words of the Form 990 instructions. Penalties keep running until an electronic return is accepted.
A neighborhood health clinic with $450,000 of gross receipts mails a paper 2025 Form 990-EZ on May 10, 2026, five days early. Because it was required to e-file, the IRS treats the return as not filed. The clinic's preparer e-files it on August 3, 2026, 80 days after the May 15 due date. For a return required to be filed in 2026, the penalty is $25 a day: 80 × $25 = $2,000. The cap would be the lesser of $13,000 or 5% of $450,000 ($22,500), so $13,000; it hasn't been reached. The clinic can ask for relief, but "we mailed it on time" is not, by itself, a defense.
When paper is still used
The e-file system accepts returns for the current tax year and the two prior tax periods. A return older than that, whether an original that was never filed or an amended return, goes on paper, with a notation at the top of page 1 that the IRS no longer accepts e-file for that year. The window rolls forward each year: the IRS stopped accepting e-filed 2020 returns as of December 26, 2023, for example.
If you are several years behind, the window decides which returns go electronically and which go on paper, so a catch-up project often involves both. Catching up on late returns explains the order to file them in.
Organizations using the streamlined reinstatement process also file paper 990-EZs for the missed years, marked "Retroactive Reinstatement."
How e-filing works, step by step
- Choose the channel. Forms 990, 990-EZ, 990-PF and 990-T go through IRS-authorized e-file software, either your preparer's or a commercial product you use yourself.
- Prepare the return and every required schedule. The e-file system checks the return against business rules, so a missing schedule usually means a rejection.
- Check the header against IRS records. The legal name, EIN and tax year must match what the IRS has on file. If your name or address changed, see changing your name, address or fiscal year.
- Have an officer sign Form 8879-TE (see below).
- Transmit, and watch for the acknowledgment.
- Save the acceptance with your copy of the return, and prepare the public-inspection copy.
Signing an e-filed return
An e-filed return still needs an officer's signature. When a preparer transmits the return, an authorized officer (for example the president, treasurer or executive director) signs Form 8879-TE, IRS e-file Signature Authorization for a Tax Exempt Entity, which authorizes the electronic signature. The preparer keeps the signed form; it isn't sent to the IRS unless requested. Form 8879-TE replaced the older Form 8879-EO.
Filing the 990-N
Small organizations, those with gross receipts normally $50,000 or less, file the Form 990-N themselves through the IRS e-Postcard system. Filers sign in with a Login.gov or ID.me account, using the same email address associated with their IRS account, and the IRS recommends using a computer rather than a phone or tablet. You need only basic information: EIN, tax year, legal name and address, any other names used, a principal officer's name and address, a website if you have one, and confirmation that gross receipts are $50,000 or less. The IRS help line for exempt organizations is 877-829-5500.
Keep the Login.gov or ID.me account tied to an organizational email address, not a volunteer's personal inbox. When a treasurer leaves, a lost login is one of the most common reasons a 990-N goes unfiled for years.
Acknowledgments and rejections
Every e-filed return comes back with an acknowledgment: accepted or rejected. A rejected return hasn't been filed. Rejections are usually technical and can be fixed and resubmitted:
| Common rejection cause | Typical fix |
|---|---|
| Name or EIN doesn't match IRS records | Use the exact legal name on file, or update it with the IRS first |
| Required schedule missing | Add the schedule triggered by Part IV (see Form 990 schedules) |
| Wrong return for the organization's size | Re-prepare on the correct form |
| Tax year outside the e-file window | File on paper with the required notation |
File early enough that a rejection can be fixed before the deadline, and use Form 8868 if you need more time.
Common mistakes
- Mailing a paper return "to be safe." It isn't safe; it counts as not filed.
- Assuming transmission means filing. Only an accepted return is filed.
- Leaving out schedules to file faster. An incomplete return can draw the same daily penalty as a late one.
- Letting e-Postcard credentials leave with a volunteer.
Frequently asked questions
Can we e-file the return ourselves?
Forms 990, 990-EZ and 990-PF are e-filed through IRS-authorized e-file providers and software, either by a preparer or by the organization using commercial software. The 990-N is different: you file it yourself on IRS.gov.
How do we know the return was received?
The IRS sends an electronic acknowledgment saying the return was accepted or rejected. Keep the acceptance with your copy of the return. A rejected return hasn't been filed until it is corrected and accepted.
We need to amend a return from four years ago. Can it be e-filed?
Probably not. E-filing is only available for the current tax year and the two prior tax periods. Older original or amended returns are filed on paper, marked as the instructions require.
Our return was rejected on the due date. Are we late?
Fix the problem and retransmit right away, and keep the rejection notice and records of the original transmission. The safest course is not to be in that position: file a week or more before the deadline, or extend with Form 8868 before the deadline passes.
Do we still sign anything on paper?
Usually just Form 8879-TE, which the officer signs and the preparer keeps. Don't mail it to the IRS unless asked.
Sources
- IRS: Annual filing and forms. irs.gov
- IRS: 2025 Instructions for Form 990, sections E and H. irs.gov
- IRS: 2025 Instructions for Form 990-T. irs.gov
- IRS: Annual electronic filing requirement for small exempt organizations (Form 990-N). irs.gov
- IRS: Publication 5248, e-Postcard (Form 990-N) user guide. irs.gov
- IRS: About Form 8879-TE. irs.gov
- IRS: Rev. Proc. 2024-40, section 3.54. irs.gov
IRS figures change; inflation-adjusted amounts are updated each year. We review this page when the IRS publishes new instructions.
990IRS.com is a private company, not the IRS. This page is general information, not legal or tax advice for your organization. Example organizations and figures are hypothetical.
