Late Form 990 filing, penalty relief and reinstatement

It happens more often than people think. A treasurer moves away, a volunteer board loses track, a founder assumes the accountant filed. Then a penalty notice arrives, a grantmaker can't find you in the IRS database, or a CP-120A letter says your exemption is gone. A nonprofit that is behind can almost always get current; the order you do things in decides how much it costs.

This service is for organizations with one or more missing Forms 990, 990-EZ, 990-PF or 990-N, organizations holding an IRS penalty notice, and organizations whose exemption was automatically revoked after three consecutive years without a required return. Our guides on catching up and automatic revocation explain the rules.

What's included

• A status check. We search your EIN in the IRS Tax Exempt Organization Search, including the Auto-Revocation List, and review any IRS letters you have.
• A filing map. Which years are missing, which form each year needed, and which can still be e-filed (the current tax year and the two prior periods) versus filed on paper.
• Preparation of the missing returns, most urgent first, so a third consecutive missed year never happens.
• Penalty notices explained: what the IRS is charging and why.
• Reasonable-cause relief requests, drafted with you from the facts and signed by an officer.
• For revoked organizations: a recommendation among the four reinstatement routes, guidance through the application for exemption, and preparation of the paper returns the route requires.
• A plan for the years while reinstatement is pending, so you know what to file and when.
• A calendar going forward, so the problem doesn't repeat.

What we need from you

• Every IRS letter or notice you've received, especially any CP-120A, with its date
• Copies of the last returns that were filed, and any IRS login or e-file records you can find
• Bank statements for each missing year
• Financial statements or bookkeeping records for those years, if they exist
• Donor and grant records, payroll records and board minutes
• Officer and director lists for each year
• A written timeline of what happened: who was responsible for filing, when that changed, and when the problem was discovered
• Supporting documents for reasonable cause, if any (medical records, disaster declarations, correspondence)

Lost records? We help you rebuild figures from bank statements, donor records and minutes, and document how they were reconstructed.

How it works

1. Short consultation about what you know and what you've received.
2. Status check and filing map, so you see the whole picture before deciding.
3. Fixed quote and checklist. Nothing starts until you approve.
4. Preparation of the missing returns and any relief request or reinstatement returns.
5. Review with you, including the reasonable-cause statement, which must be accurate and specific.
6. Signatures. An officer signs Form 8879-TE for e-filed returns, and signs paper returns and relief statements directly.
7. Filing and follow-up. We file, send you the confirmations and help you answer what the IRS sends next.

Deadlines to know

Late Forms 990, 990-EZ and 990-PF carry a daily penalty. For returns required to be filed in 2026 it is $25 a day up to the lesser of $13,000 or 5% of gross receipts, or $130 a day up to $65,000 for organizations with gross receipts over $1,309,500. A late 990-N has no penalty. Penalty notices have a response date; reply by it. Our penalty calculator estimates the exposure.

For revoked organizations the key date is 15 months after the later of the CP-120A letter or your appearance on the Revocation List. The streamlined route and the easier retroactive route are only available within that window. The automatic revocation checker helps you see where you stand.

When this gets more complex

Choosing a reinstatement route. Rev. Proc. 2014-11 offers four:

Every route requires Form 1023, 1023-EZ, 1024 or 1024-A and the user fee ($600 for Form 1023, $275 for Form 1023-EZ). The retroactive routes call for paper returns for the three missed years and later years due before the application, marked "Retroactive Reinstatement."

Filing while reinstatement is pending. Until exemption is restored, the organization is treated as taxable and may have to file Form 1120 or 1041. Which returns make sense for those interim years depends on the route and the date you expect to be reinstated back to; we work that out with you.

Organizations behind on more than the 990, such as a 990-T or state renewals, need the same mapping.

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.