Missing Form 941 filings since Q2 2021 but paid taxes via QuickBooks and filed W-2s - What to do about IRS notice?

This is unfortunately a common issue with businesses winding down. Payments don't replace the need for filing the actual forms. When you pay through QuickBooks, you're handling the tax deposits, but you still need to submit the 941 forms quarterly to report those payments. The IRS showing $0 for W-2 wages likely means they didn't process your W-2/W-3 forms correctly or they weren't received. The 941 forms and W-2/W-3 forms go through different processing systems at the IRS, and they later cross-reference them. Here's what you should do: First, gather all your quarterly payroll reports from QuickBooks for 2021. Then prepare and file the missing 941 forms for Q3 and Q4 2021 (and any quarters after that if missing). You'll need to mail these with a brief explanation letter. Also, send copies of all your 2021 W-2s and the W-3 summary form as requested. Be prepared for some late filing penalties, though you might be able to request an abatement since you did pay the taxes on time. The IRS has reasonable cause provisions that might help in your situation.

I went through something similar last year and found https://taxr.ai incredibly helpful. My accountant also messed up our 941 filings but had processed payments. I was totally lost trying to figure out which forms were actually filed versus just paid. The taxr.ai service analyzed all my QuickBooks records and IRS notices and clearly showed me which quarters were missing filings versus just payment discrepancies. It saved me hours of digging through old records and helped me understand exactly which forms I needed to file retroactively. The best part was they explained everything in simple terms rather than tax jargon. After using their analysis, I was able to file the missing quarters and respond precisely to the IRS notice with supporting documentation they recommended.

After seeing the recommendation here, I decided to try taxr.ai for my own tax notice problem. I was genuinely surprised by how helpful it was! I uploaded my confusing IRS notice and some QuickBooks reports, and they sent back a really clear explanation of which forms were missing and exactly what information needed to go on each one. The analysis showed that I had a similar issue - payments made through QuickBooks but several unfiled 941s. They even pointed out a calculation error in my W-3 that would have caused problems later. Using their guidance, I filed all the missing forms last week and included the explanation letter they suggested. The IRS already responded saying they're processing my correction. If you're struggling with this reconciliation issue, it's definitely worth checking out.

I had a nightmare situation with unfiled 941s for my small business last year. After getting nowhere with the IRS phone lines for weeks (always disconnected or 2+ hour waits), I tried https://claimyr.com and it was a game-changer. They got me connected to an actual IRS agent within 20 minutes! The agent was able to tell me exactly which quarters were missing and gave me specific instructions on how to file the late returns. She even noted in my file that I had called and was working to resolve the issue, which apparently helps prevent further escalation. You can see how it works here: https://youtu.be/_kiP6q8DX5c Without getting through to an actual person at the IRS, I would have been guessing which forms were really missing versus just not showing up in their system yet.

I was totally wrong about Claimyr! After posting my skeptical comment, I decided to try it anyway since I was desperate to resolve my own tax issue. It actually worked exactly as described - I got a call back in about 45 minutes, and when I answered, I was connected directly to an IRS representative. The agent was able to confirm which specific 941 forms were missing from my account and gave me detailed instructions for submitting them. She also explained that I qualified for the first-time penalty abatement program since I had a clean compliance history before this. I was able to resolve in one phone call what I'd been stressing about for weeks. Would never have gotten through without this service. Definitely recommend it if you need to actually speak with someone at the IRS about your missing forms.

Former payroll specialist here. One thing to watch out for - if you filed your W-2s through QuickBooks, make sure you check if they were actually transmitted to the SSA. Many small businesses think QuickBooks automatically files these forms, but sometimes you need to take an additional step to submit them. If QuickBooks did transmit them, you should have received a confirmation. The SSA then sends that W-2 data to the IRS, which is why they're saying they don't match your 941s. If you can't find a confirmation that your W-2s were submitted, you might need to resubmit those as well. Also, the IRS will likely charge you "failure to file" penalties for the missing 941s, even if you paid the taxes. These can be substantial - 5% of the unpaid tax for each month the return is late, up to 25%.

Has anyone successfully gotten the IRS to waive penalties for late 941 filings? I'm in a similar position but afraid of getting hit with thousands in penalties even though we paid everything on time.

I'm dealing with a very similar situation right now! My small business also used QuickBooks for payroll and tax payments, but somehow we missed filing several 941 forms in 2022. I just got an IRS notice last week showing discrepancies between our W-2s and what they have on file for quarterly returns. One thing I learned from calling the IRS Business Tax Line is that they have a specific department for employment tax issues (different from individual tax problems). The representative told me that as long as you can show you made the payments on time through EFTPS or QuickBooks, they're usually willing to work with you on penalty abatement. She also mentioned that many small businesses run into this exact issue when winding down operations - the focus shifts to closing everything up and sometimes the quarterly filings get overlooked even though the payments continue automatically. I'm planning to gather all my QuickBooks payment confirmations and file the missing quarters this week. The IRS gave me 30 days to respond to their notice, but they said filing sooner rather than later shows good faith compliance.