CPA Filed Tax Return under Wrong EIN Number - Can This Be Fixed?

This is actually more common than you'd think, and while it's definitely something you need to address, it's fixable! The IRS has procedures for exactly this situation. You'll need to file amended returns (Form 1120X for corporations or 1040X for individual returns with business income) with the correct EIN. Make sure to include a detailed explanation letter clearly stating what happened - that your CPA accidentally transposed a digit in your EIN. Contact the IRS Business & Specialty Tax Line at 800-829-4933 to alert them to the situation. They can help ensure your tax payments are properly credited to your correct EIN. Have all your documentation ready, including copies of your previously filed returns, proof of your correct EIN (your original EIN assignment letter), and proof of payments made. Since the payments were actually made, even though under a slightly incorrect identifier, the IRS is usually reasonable about waiving penalties if you're proactive about fixing the error. Document all your communications with them.

Went through something similar last year with my restaurant business. My accountant transposed two digits on our EIN and we only found out because we got a weird notice from the IRS about missing quarterly payments (which we definitely made). I was stressing hardcore, but I found this amazing service called taxr.ai that literally saved me from this nightmare. I uploaded our tax documents to https://taxr.ai and their system immediately flagged the EIN discrepancy and gave me a detailed explanation of what needed to be fixed. They have this AI that reviews all your forms and transcripts to find mistakes like this. The system actually generated the explanation letter we needed for the IRS explaining the error. Made the whole process of filing the amended returns so much clearer.

Just wanted to follow up about taxr.ai since I posted that skeptical comment earlier. I actually ended up trying them for my situation (small construction business, CPA messed up our EIN digits). I'm honestly blown away by how helpful they were. Their system found not just the EIN issue but also flagged that my CPA had been using the wrong business code for our industry which could have caused problems down the line. The report they generated made everything crystal clear, and I was able to get amended returns filed with all the proper documentation. Their explanation letter template for the IRS was super professional - my new accountant said it was better than what she would have drafted. Just wanted to share since I was wrong to be so skeptical before.

Have you tried calling the IRS directly? I had to do that for a similar issue and spent WEEKS trying to get through to someone who could actually help. Kept getting bounced between departments, waiting on hold for hours only to get disconnected. It was a complete nightmare. Finally found this service called Claimyr that got me through to an actual IRS agent in less than 20 minutes. Check them out at https://claimyr.com - they have this system that navigates all the IRS phone menus and waits on hold for you, then calls you once an agent is on the line. You can see how it works in this video: https://youtu.be/_kiP6q8DX5c Seriously saved me so much time and frustration. The IRS agent I spoke with was able to note my account about the EIN issue and gave me specific instructions on how to submit the amended returns to make sure they were processed correctly.

Ok I have to admit I was completely wrong about Claimyr. After posting that skeptical comment, I decided to try it myself since I was getting nowhere with the IRS on my own for a similar EIN issue. The service actually works exactly as advertised. I got a call back in about 35 minutes with an actual IRS agent on the line ready to help me. The agent was able to verify my information, confirm the EIN discrepancy in their system, and give me clear instructions on how to submit my amended returns with proper documentation. Saved myself literally days of frustration. My EIN issue is now being resolved and I have a direct case number to reference. Sometimes being skeptical makes you miss out on solutions that actually work.

I'm a bookkeeper and have seen this happen a few times with clients. One thing not mentioned yet - you should also check if your state tax returns were filed with the incorrect EIN, as this could cause issues with state taxes as well. Many states use your federal EIN for their systems. Also, double check that your payroll tax reports (941s, 940, W-2s, etc.) were filed with the correct EIN. If those were also filed incorrectly, you'll need to address those separately from your income tax returns.

Check your state's Secretary of State business registry too! If your CPA used the wrong EIN on any official business filings, it could affect your business's standing. I had this happen and almost lost our LLC's good standing because notices were being associated with a non-existent business ID.

Don't panic - this is definitely fixable! I went through almost the exact same thing with my landscaping business last year. My CPA had been filing with a transposed digit for THREE years before we caught it. Here's what I learned from the experience: First, get your original EIN assignment letter from the IRS (you can request a copy online if you don't have it). Second, gather all your payment confirmations showing you actually made the tax payments - this proves good faith compliance even with the wrong number. The IRS was surprisingly understanding once I explained the situation. They have a specific procedure for EIN corrections and they see this more often than you'd think. File your amended returns ASAP with a clear explanation letter attached. Include phrases like "inadvertent clerical error by tax preparer" and "taxpayer remained in full compliance with all tax obligations." One thing that really helped me was keeping detailed records of every phone call and correspondence with the IRS. Get reference numbers for everything. The whole process took about 3-4 months to fully resolve, but no penalties were assessed since I was proactive about fixing it. Your CPA should absolutely help you fix this at no charge since it was their error. If they refuse, find someone else - this kind of mistake shows they're not being careful with your critical information.

I'm a tax professional and see this issue come up a few times each year. The good news is that the IRS has streamlined procedures for EIN corrections, and they're generally very reasonable about these situations when taxpayers are proactive. One important point I haven't seen mentioned yet - make sure to check your quarterly estimated tax payments as well. If those were also made under the incorrect EIN, you'll want to document those payments when you contact the IRS so they can properly credit them to your correct account. Also, consider requesting a "wage and income transcript" from the IRS for both EINs (the correct one and the incorrect one your CPA used) to see exactly what information they have on file. This will help you understand the full scope of what needs to be corrected. When you file your amended returns, I strongly recommend sending them via certified mail with return receipt requested. This gives you proof of when the IRS received your corrections, which can be important if there are any timing issues. Finally, once this is resolved, make sure your CPA implements some kind of verification process to prevent this from happening again. Something as simple as having you review and sign off on the EIN before filing could prevent future issues.

I went through this exact nightmare two years ago with my HVAC business! My CPA had been filing with two digits swapped in our EIN for an entire year. I was absolutely panicking when I discovered it during a bank loan application. Here's what worked for me: First, don't wait - contact the IRS Business & Specialty Tax Line immediately at 800-829-4933. Have your correct EIN assignment letter, copies of all tax returns filed with the wrong EIN, and proof of all payments made ready when you call. The agent I spoke with was actually very helpful and walked me through the entire correction process. You'll definitely need to file amended returns (1120X or 1040X depending on your business structure) for both 2022 and 2023. The key is including a detailed explanation letter with each amended return clearly stating this was an inadvertent error by your tax preparer. Use language like "clerical error in EIN transcription" and emphasize that all tax obligations were met in full and on time. The IRS agent told me they see this more often than people think, especially with single-digit transpositions. Since you made all your payments and were compliant with filing deadlines, they should waive any penalties. The whole process took about 3 months for me, but I had no penalties assessed. Also, definitely make your CPA handle all the paperwork for this correction at no charge since it was their mistake. If they push back on that, find a new tax professional who will be more careful with your critical business information.

I'm a small business owner who went through something very similar about 18 months ago. My bookkeeper had been using an incorrect EIN (off by one digit) for almost two full tax years before we caught it during a routine review. The most important thing is to act quickly and be completely transparent with the IRS. I called their Business & Specialty Tax Line and the agent was actually quite helpful once I explained it was an honest clerical error by my tax preparer. Here's my step-by-step process that worked: 1) Gathered all documentation - original EIN letter, copies of incorrectly filed returns, proof of all payments made, 2) Called the IRS to report the error and get a case number, 3) Filed amended returns with detailed explanation letters for each affected year, 4) Followed up regularly until everything was resolved. The whole process took about 4 months, but no penalties were assessed since I was proactive and could prove all taxes were actually paid on time. The IRS sees these EIN transposition errors more frequently than you'd think. One critical tip - make sure to check ALL your filings, not just income tax returns. This includes quarterly payroll reports (941s), annual unemployment reports (940), and W-2s. If any of those used the wrong EIN, you'll need to file corrections for those as well. Your CPA should absolutely handle this correction at no cost since it was their error. If they won't take responsibility, consider finding someone more reliable for future filings.