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This guide walks you through what can be amended, how to file an amended return, and specific procedures for each variant of the form.
Whether you’re a large nonprofit or a small organization, filing IRS Form 990 correctly is crucial for maintaining tax-exempt status and public trust. But what if you discover a mistake after the IRS has already accepted your return? Don’t panic — the IRS allows you to file 990 amendments. This guide walks you through what can be amended, how to file an amended return, and specific procedures for each variant of the form.
Which 990 forms can be amended?
You can file an amendment for most of the 990 forms except Form 990-N, which includes:
- Form 990-EZ — For organizations with gross receipts less than $200,000 and assets less than $500,000.
- Form 990 – For organizations with gross receipts greater than or equal to $200,00 (or) assets less than or equal to $500,000.
- Form 990-PF – For private foundations.
- Form 990-T – For organizations with unrelated business income of $1000 or more.
📌How to amend Form 990-N?
You cannot file an amended Form 990-N. You can make corrections or update your information when you file your next e-postcard in a subsequent year.
What information can be amended?
You can amend any part of your original 990 forms as long as the IRS accepted the return. The most common sections include:
- Financial data
- Program details
- Officer information
- Attached schedules
However, you cannot amend the organization’s EIN (Employer Identification Number). If your EIN was entered incorrectly on the original return, you’ll need to contact the IRS directly to correct it, as it is a permanent identifier that cannot be changed through an amended return.
When is the deadline for filing amendments?
There’s no specific IRS-imposed deadline for amending Form 990, but it’s recommended to file an amendment as soon as an error is identified. Timely correction is essential not only for maintaining accurate records with the IRS but also for ensuring consistency across other areas where your Form 990 may be referenced, such as state compliance filings, grant applications, annual reports, and donor communications.
If inaccurate information remains uncorrected, it can lead to discrepancies that may raise concerns with funders, regulators, or watchdog organizations. Promptly filing an amended return helps preserve your organization’s credibility, supports transparency, and reinforces public and stakeholder trust in your operations.
How to file an amendment?
If you discover an error after submitting your Form 990, follow these steps to file an accurate, amended return:
1. Use the same tax year form
Ensure you use the same version and tax year of the form you originally filed. Use it as the base to make corrections.
2. Mark the return as ‘Amended’
Indicate that the return is being amended by checking ‘Amended Return’ at the top of the first page.
3. Update the incorrect sections
Only the parts that need correcting must be updated, but many choose to resubmit the entire return for clarity. Always ensure consistency across parts (e.g., correcting revenue in Part VIII should also reflect in Part I).
4. Explain the changes in Schedule O
Whenever you file an amended Form 990 (including 990-EZ or 990-PF), you must include Schedule O — the ‘Supplemental Information’ section. Think of it as the narrative explanation page that tells the IRS exactly what changed and why.
- What was incorrect?
Briefly identify the error, including the form part and line number (e.g., ‘Part VIII, Line 1g – overstated contributions due to duplicate entry’). - What is the corrected information?
State the accurate value or detail being corrected, and mention any affected schedules (e.g., ‘Corrected total is $25,000; Schedule B updated accordingly’). - Why is the amendment being filed?
Explain the reason for the correction in a sentence (e.g., ‘Filed due to bookkeeping error discovered during audit’). - E-File the amended return
Most exempt organizations must file electronically. Use an IRS-authorized e-file provider. If you filed the original return on paper, the amendment should still be e-filed if e-filing is now required.
Click here to view how to amend a Form 990 with Tax990.
File amendments for free, backed by The Tax990 Commitment!
With the Tax990 Commitment, you’re always covered — even after you file. If you discover any mistakes on your 990 forms submitted through Tax990, you can file corrections at no extra cost.
We securely save your original return, so when it’s time to make a correction, there’s no need to start from scratch. We pre-fill everything that’s already correct — you just update the parts that need fixing. It’s fast, simple, and stress-free.
Whether you’re correcting a number, adding a missed schedule, or updating board info, you can amend with confidence — and without any extra charges.
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