Internal I-9 Audits: Best Practices

Internal I-9 audits are one of the easiest ways to reduce compliance risk before it becomes a bigger issue. Even strong HR teams can end up with gaps—especially with remote onboarding, turnover, and busy hiring seasons. The good news? If you handle an internal audit the right way, you can correct many issues without creating new problems.

Below are practical best practices for running an internal I-9 audit—and guidance on one of the most common questions: What if Section 2 was never completed at the time of hire?

Why conduct an internal I-9 audit?

A proactive I-9 audit helps you:

• Confirm you have Forms I-9 on file for employees who require them
• Identify missing or incomplete sections early
• Fix errors using compliant correction methods
• Show good-faith compliance if your organization is ever inspected

Best practices for conducting an internal I-9 audit

1) Set your audit scope and stay consistent

Start by deciding what you are auditing:

• All I-9s, or
• A neutral subset, such as all hires from a specific date range or location

Consistency is key. Your audit method should be non-discriminatory and applied the same way across the group you’re reviewing.

2) Keep I-9 forms separate from personnel files

Best practice is to store I-9s in a dedicated system (paper or electronic) rather than inside personnel files. This helps you:

• Limit access to sensitive data
• Respond quickly if an agency requests I-9s
• Avoid exposing unrelated employee information

3) Use a standard checklist for every form

A checklist keeps your audit organized and ensures you’re reviewing the same items across the board. Prioritize the most common risk areas:

• Missing I-9 entirely
• Section 1 incomplete or missing signature
• Section 2 incomplete, missing, or late
• Missing employer signature/date
• Document details missing or inconsistent
• Reverification issues (when required)

4) Correct errors properly (and never backdate)

When correcting an I-9:

• Do not backdate
• Do not use white-out
• Do not erase
• Correct by drawing a single line through incorrect information, entering the correct info, and adding initials and the date of the correction.

If you are attaching a memo or explanation, keep it brief and factual.

5) Avoid discrimination risks during the audit

Audits can accidentally create risk if handled inconsistently. A few guardrails:

• Don’t request specific documents. Employees can choose which acceptable documents to present.
• Don’t require “extra” documents beyond what the form requires.
• Apply the same correction process for everyone in the audit scope.

6) Document the audit process

Keep a short internal audit record showing:

• Audit dates and reviewer(s)
• Which I-9s were included (and how they were selected)
• What checklist was used
• How corrections were handled
• A summary of what was fixed and what still needs follow-up

This kind of documentation demonstrates good-faith compliance and helps your team stay consistent.

What if Section 2 wasn’t completed at the time of hire?

This is a common discovery during internal audits. In most cases, the best practice is:

✅ Complete Section 2 now — and document what happened

If the employee is currently employed, you typically should complete Section 2 as soon as possible using the proper correction approach, rather than leaving it blank and only noting the issue.

Here’s the recommended approach:

1. Have the employee present acceptable documentation now
   The employee chooses which acceptable documents to present from the approved lists.
2. Complete Section 2 based on what you review now
   Record the document information accurately.
3. Use today’s actual date — do not backdate
   The point is to show that the verification was completed late, but honestly.
4. Add a brief written explanation
   Example:
   “During an internal audit on [date], we discovered Section 2 was not completed within the required timeframe. Section 2 was completed on [date] after review of acceptable documents. No backdating.”

When a new I-9 may be appropriate

If the original I-9 is unusable (missing too much information, damaged, or otherwise unreliable), it may be better to complete a new I-9. If you do, keep the old one and attach a simple explanation of why a new form was completed.

Final takeaway

Internal I-9 audits don’t have to be scary — they just need to be consistent, well-documented, and handled carefully. If you discover that Section 2 was missed at hire, the best practice is usually to complete it now using correct procedures, document the reason, and avoid backdating.

If you’d like, we can turn this into a one-page SOP + checklist your team can follow during quarterly audits.

I hope this helps.