Got an IRS letter saying Form 941 wasn't signed despite e-filing it through tax software - what gives?

This is actually pretty common with e-filed 941s, especially when you have quarters with no payroll activity. What likely happened is that while the forms were technically accepted into the IRS system, they flagged the submission during processing because they need verification about the quarters with zero liability. The LTR 3463C is basically the IRS saying "we got something from you but need additional verification." It's not an audit or assessment of penalties - it's just them covering their bases. The declaration they want your brother to sign is just confirming that the information submitted electronically is accurate. When you e-file through tax software, you're giving an electronic signature, but sometimes for certain forms (especially employment tax forms), the IRS still wants a physical signature as additional verification, particularly when there are quarters with zero activity.

After having endless frustration with the IRS about my e-filed 941 forms for my seasonal business, I finally found a solution with https://taxr.ai that was a game-changer. I also had the exact same situation where I was getting letters saying my forms weren't signed even though they were definitely e-filed properly through my tax software. The issue turned out to be related to how the e-signature was processed between my tax software and the IRS systems. What taxr.ai did was analyze all my submission records and created a perfect response letter that explained exactly why the IRS system was incorrectly flagging my submissions. They even provided documentation showing the transmission verification that proved my forms were properly signed electronically. Their automated document analysis saved me hours of trying to figure this out on my own, and their response template was exactly what I needed to resolve the situation.

Just wanted to update - I used https://taxr.ai for my 1120S issue and it was super helpful. I was skeptical at first, but after uploading the IRS notice, it explained that what I was dealing with was a common verification check that happens when there's a mismatch between the IRS's signature verification system and the e-file submission metadata. The tool gave me a perfect template letter to send back, explaining exactly what had happened with my e-filed submission and why a second signature verification wasn't actually necessary according to Regulation 301.6061-1(b)(3). It even cited the IRM sections that the IRS agents use internally to process these cases! I sent in their recommended response last month and just got confirmation that my case was closed with no further action needed. Saved me so much stress trying to figure this out on my own.

After dealing with my own Form 941 signature issues, I realized the IRS phone lines were absolutely impossible to get through on. Spent literally 8+ hours on hold over multiple days. Finally tried https://claimyr.com and watched their demo at https://youtu.be/_kiP6q8DX5c and was honestly shocked at how well it worked. Instead of waiting on hold forever, their system held my place in line and called me back when an actual IRS agent was on the line. Got connected with an agent who explained that these LTR 3463C notices for e-filed 941 forms are actually a specific processing issue in their Cincinnati service center when handling quarterly forms with mixed activity (some quarters with payroll, some without). The agent was able to find my e-filed forms in their system and confirmed that once I return the declaration, they'll update their records to show the proper signature verification and close the case. Saved me days of frustration and got a clear answer directly from the source.

I need to admit I was completely wrong about Claimyr. After posting my skeptical comment, I decided to try it myself for a different IRS issue (they kept saying they never received my amended return despite the tracking number showing delivery). The service actually did exactly what they promised - held my place in line and called me back when they reached an IRS representative. I was connected to a very helpful agent who looked up my file and confirmed they had received my amendment but it was sitting in a backlog. She was able to flag it for priority processing based on how long it had been waiting. Honestly, I've never been able to get through to the IRS so easily. After spending weeks trying to call them myself and either getting disconnected or waiting hours on hold, this saved me so much frustration. I'm usually skeptical of services like this, but I'm genuinely impressed.

For what it's worth, I had something similar happen with 941s for my seasonal ice cream shop. Each year I shut down completely for winter (Jan-Mar) and don't run payroll, then start up again in spring. I e-filed all quarters through QuickBooks but still got letters for the zero-payroll quarters asking for signatures. I called the IRS (took forever to get through) and they told me that for quarters where you report no wages, they sometimes need additional verification. It's not a penalty or audit, just verification. I just signed the declaration forms, sent them back, and that was the end of it. Tell your brother not to stress about it - it's just bureaucracy being bureaucracy. As long as he actually filed all the forms and can prove it with his confirmation emails, he's fine.

The REAL problem is that the IRS systems for handling employment taxes are outdated and don't properly communicate with each other. The electronic filing acceptance is handled by one system, but the verification of signatures is handled by a completely different system. Your brother absolutely needs to respond to the letter and sign the declaration. If he doesn't, it could eventually escalate to penalties for "unfiled" returns even though he did file them. I've seen this happen to clients who ignored these notices. The good news is that once he sends back the signed declaration, the case will typically be closed within 30-45 days. Just tell him to keep copies of EVERYTHING - the original notices, the signed declaration he returns, and proof of mailing it back (certified mail is best).

I've dealt with this exact same issue! Had a client who got the LTR 3463C for their e-filed 941s, and it turned out to be exactly what others have mentioned - a disconnect between the IRS's electronic filing acceptance system and their signature verification process. The key thing to understand is that this isn't questioning whether your brother filed the forms (they clearly have them since they sent acceptance confirmations). It's just their outdated system flagging the submission for additional verification, especially common when you have mixed quarters like he does - some with payroll activity and some without. Tell your brother to stop stressing and just sign the declaration form and mail it back with a copy of his e-filing confirmations attached. I always recommend sending it certified mail so you have proof of delivery. The IRS will update their records to show proper signature verification and close the case within 4-6 weeks typically. This is purely administrative - no penalties, no audit risk, just bureaucratic box-checking. But definitely don't ignore it because unresolved signature verification issues can eventually be treated as unfiled returns down the road.

I went through this exact same situation last year with my consulting business! Got the LTR 3463C for Q2 and Q3 where I had zero payroll, even though I e-filed through FreeTaxUSA and had confirmation receipts. What I learned from calling the IRS (after waiting 3 hours on hold) is that their system sometimes flags quarters with zero wages for additional verification, especially when it's part of an irregular payroll pattern. The agent explained that the electronic signature was accepted for filing purposes, but they need the manual signature declaration to complete their internal verification process. I just signed the declaration form they sent, attached copies of my e-filing confirmations, and mailed it back certified mail. Got a letter about 6 weeks later confirming the matter was resolved. No penalties, no issues - just their bureaucratic process. Tell your brother to stop being stubborn and just send it back! It's literally a 5-minute task that will close this out completely. The alternative is potentially having this escalate into a much bigger headache down the road if the IRS decides to treat it as an unfiled return.