IRS Matching Issues: What They Are and How to Avoid Them

When you’re self-employed and managing your business’s taxes, one of the most frustrating complications you can encounter is an IRS matching issue. These discrepancies between what the IRS has on record and what you report on your tax return can lead to notices, reassessments, and a lengthy back-and-forth process.

This guide explains what matching issues are, what causes them, and how you can prevent them.

What is an IRS Matching Issue?

A matching issue occurs when the IRS’s records differ from what you reported on your tax return.

The IRS receives information returns—like Form 1099-NEC—from your clients throughout the year. These forms report payments made to you and include the tax identification number (TIN), either your Social Security Number or EIN, where that income was sent.

When you file your tax return, the IRS compares what you reported against the information they received from third parties. If there’s a discrepancy, you have a matching issue.

Why this matters: Regardless of how you file your tax return, the IRS maintains records of payments from clients assigned to a particular tax ID, and that’s where they expect that income to be sourced or reported for tax purposes.

Common Causes of Matching Issues

Matching issues are typically caused by a mismatch between your business’s tax status, your EIN, and the information your clients have on file.

Outdated W-9 Forms with Clients

When you form an LLC and receive a new EIN, but don’t inform existing clients that you’re now receiving payments to a new tax ID, it creates matching issues.

Those clients will continue issuing 1099s to your Social Security Number (SSN) or old sole proprietor EIN. The IRS then has records showing income assigned to your personal SSN, while you are reporting that same income on your LLC’s tax return.

Mid-Year Business Structure Changes

Structure changes during the tax year present particular challenges.

If you switched your business structure mid-year (e.g., from Sole Proprietor to an LLC with S Corp election) but never told your clients that payments should now go to an LLC EIN, that client is going to issue you a 1099 for the full year to your old TIN.

This creates matching issues where the IRS expects you to report that income tied to one tax ID versus the other.

• For Sole Proprietors forming an LLC (LLC Tier Members) The key change is that you are moving from a structure where payments were likely tied solely to your SSN to an entity that primarily uses an EIN. If clients don’t update their records, payments made after your formation date may still be reported under your SSN
• For Sole Proprietors forming an LLC and Electing S Corp (S Corp Tier Members) This transition involves the biggest change to your tax profile. You move from reporting business activity on your personal return to reporting it on a separate business tax return tied to the LLC EIN. This is a critical point for client reporting.

Payments to Business Bank Accounts without Proper Notification

This mistake happens when you open a new business bank account under your LLC EIN and start depositing client payments there, but never tell your clients to update your EIN.

Your clients are still going to issue 1099s to your SSN instead of your EIN. When tax time comes, you have a mismatch between what’s reported on your business tax return and what the IRS has on record.

Changes to S Corp Status

When your business forms an LLC and elects S Corp status, you now report that business activity on a separate business tax return (Form 1120-S), assigned to that LLC EIN. If you haven’t told your clients that you’re under a new EIN, they’ll continue to issue 1099s to your old TIN. This is a common matching issue following a tax status change.

How the IRS Responds to Matching Issues

When the IRS identifies a discrepancy between their records and your tax return, here’s what typically happens:

• IRS notices: The IRS will send notices questioning your tax reporting.
• Reassessment of your tax bill: The IRS may reassess your tax bill based on their records rather than what you reported, potentially resulting in additional tax owed.
• Back-and-forth correspondence: You’ll find yourself sending notices and letters to the IRS to explain your tax reporting.
• Forced corrections: The IRS can make their decision based on their records and force you to correct your filing.

Prevention Strategies

Matching issues are largely preventable with proper planning and communication.

• Update your W-9 forms: When you form a new business with a new tax ID, inform your clients and provide new Form W-9s so they send payment to the correct EIN. This single step prevents most matching issues.
• Open a new business bank account: Establish a new business bank account under your new tax ID. This ensures business transactions flow through accounts properly associated with your LLC EIN.
• Communicate structure changes promptly: When you form an LLC or elect S Corp status, notify clients as soon as possible so they can update their records before issuing year-end tax forms.
• Keep detailed records: If you make a mid-year structure change, document the timing and maintain clear records of which income was earned under which structure.
• Consider timing: When possible, time major structure changes at the beginning of a tax year rather than mid-year. This simplifies tax reporting.
• Verify client records: Follow up with major clients to confirm they’ve updated their records with your new tax information before year-end.

Key Takeaways

• A matching issue occurs when IRS records differ from what you report on your tax return.
• Common causes include outdated W-9 forms, mid-year structure changes, and S Corp elections without proper client notification.
• The IRS responds with notices, reassessments, and may require corrections to your filing.
• Prevention requires proactive communication: update W-9 forms, notify clients of structure changes, and maintain separate banking under your correct tax ID.
• Timing structure changes at the beginning of a tax year can simplify reporting.
• At Collective, we help members navigate business structure changes and tax reporting requirements, providing guidance to help you avoid common pitfalls like IRS matching issues.