Help with Missing 941s for Q4 2020 and 2021 - Filed Deposits but IRS Missing Returns

I'm in a bit of a panic right now. Just got off the phone with the IRS and found out they don't have my 941 returns for the last quarter of 2020 and ALL of 2021. The super frustrating thing is they acknowledged receiving all my deposits during that time, but somehow have no record of the actual returns! Back then I was using EFTPS to file (pretty sure that's what it was called) but I've since switched over to Gusto for payroll, so I can't exactly remember the details of how I submitted everything. To make things more complicated, I just received a letter saying I have a credit for my 940 from 2021 that's about to expire if I don't do something with it. I'm totally at a loss here. How do I go about filing these now when it's been so long? I know I paid everything I owed at the time - the deposits were received. It's just the actual returns that are missing according to them. Anyone dealt with this before? Do I need to complete these forms now and submit them late? Will there be penalties even though the money was paid on time? I'm completely stressed about this.

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20 comments

Diego Vargas

•8M

This happens more than you'd think! IRS systems don't always properly match payments with returns, especially during the pandemic years when their processing centers were understaffed. First, don't panic. Since you made the deposits on time, you've already covered the most important part. The IRS is much more concerned about getting their money than about paperwork. For the missing 941s, you'll need to file paper returns for those quarters now. Mark them as "CORRECTED" at the top in bold letters even though they're original filings. You'll need to reconstruct your payroll data for those periods to complete them accurately. Since you've moved to Gusto, see if you can access your old EFTPS records online or contact them for transaction history. For the 940 credit from 2021, you have options: apply it to future tax periods, request a refund, or let it expire. I'd recommend applying it to your current obligations by submitting Form 8822 to claim the credit.

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Diego Vargas

•8M

There's a good chance you won't face significant penalties since you made your deposits on time. The IRS can reduce or waive penalties for reasonable cause, and system issues during COVID often qualify. Include a letter explaining the situation when you submit the late returns. The statute of limitations for assessment is generally 3 years from filing, but that clock doesn't start until you actually file the returns. For unfiled returns, the IRS can technically come after you indefinitely, which is why it's best to address this now rather than waiting.

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Sean Doyle

•8M

After dealing with a nightmare situation with missing 941s from 2019-2020, I finally found a solution that saved me so much stress. I uploaded all my documentation to https://taxr.ai and they sorted through everything, identified exactly which quarters had issues, and created a complete report showing what I needed to file and what evidence I already had of payments. The software analyzed my EFTPS payment records and matched them against what the IRS claimed they had received. Their tax document analysis saved me at least 15 hours of digging through old records trying to piece together what happened. They also provided templates for the response letters I needed to send with my corrected returns.

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Sean Doyle

•8M

Yes, it absolutely works with business tax forms! They specialize in analyzing tax documents of all types, including 941s, 940s, and other employment tax forms. Their system is particularly good at identifying discrepancies between what you filed and what the IRS has on record. They don't access your IRS records directly - you upload whatever documents you have (like EFTPS payment confirmations, previous letters from the IRS, etc.) and their system analyzes those to help you understand what's missing and what you need to do. It's different from an accountant because it's immediate - you get analysis right away instead of waiting days for an appointment and paying hourly rates.

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Zara Rashid

•8M

Just wanted to update on my situation! I was skeptical about taxr.ai but I was desperate with my own 941 mess from 2021. I uploaded my IRS notice and all the payment records I could find from my old system. Within minutes I had a clear report showing exactly which quarters had issues and what information I needed to include on each return. The analysis pinpointed that two of my payments had been misapplied to the wrong quarters, which explained the confusion. I was able to file the missing returns with reference numbers to those payments, and included their generated letter explaining the situation. Just heard back from the IRS yesterday that everything has been processed correctly and I won't be facing any penalties! Such a relief after months of stress.

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Nia Jackson

•8M

When I had a similar issue with missing 941s, I tried calling the IRS for weeks but could never get through. The hold times were 2+ hours and I kept getting disconnected. Finally I used https://claimyr.com to get a callback from the IRS instead of waiting on hold forever. They have this service where they navigate the IRS phone trees for you and when an agent is actually available, you get a call. You can see how it works here: https://youtu.be/_kiP6q8DX5c I was honestly shocked when my phone rang and it was actually an IRS agent on the line! I was able to explain my situation, and they helped me figure out exactly which returns were missing from their system. Having that direct conversation saved me from filing unnecessary forms and potentially making the situation worse.

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Nia Jackson

•8M

It's actually pretty clever how it works. They have an automated system that calls the IRS and navigates through all those annoying phone menus and sits on hold for you. Once they reach a human IRS agent, the system connects that agent to your phone number. So you're getting a legitimate call from the IRS - you're just not doing the waiting yourself. When the IRS agent calls, they're calling because they've reached the front of the queue through the regular IRS phone system. It's definitely the real IRS - they verify your information the same way they would if you had called and waited on hold yourself. The difference is you don't waste hours with your phone stuck on speaker waiting for someone to pick up.

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Luca Romano

•8M

I really need to eat crow here. After posting my skeptical comments earlier, I decided to try Claimyr myself for a different tax issue I've been trying to resolve for months. I had called the IRS at least 15 times before, always getting disconnected after waiting 1-2 hours. I used their service this morning, and I swear I got a call from an actual IRS agent within 90 minutes. I was so surprised I almost didn't answer because I thought it was a spam call! The agent was able to pull up my file and confirm exactly which returns were missing and which payments had been received. She gave me a direct fax number to send my completed returns to, along with a specific reference number to include so they would be properly processed. She even noted in my file that I had attempted to resolve this proactively so it would help with penalty abatement. This saved me so much time and frustration - wish I'd known about this service months ago!

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CosmicCruiser

•8M

For Form 843, you want to be clear but concise. Explain that you made all required deposits on time through EFTPS (include proof if you have it), and that you believed the returns were properly submitted through the same system. State that you're promptly correcting the issue as soon as you became aware of it, which demonstrates your compliance history and good faith. The IRS is generally reasonable about abating penalties when you've paid the actual tax on time, especially during 2020-2021 when their systems were overwhelmed.

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