How to get refund after paying a Notice of Deficiency (CP3219N) in full?

I'm in a weird situation with the IRS and could use some advice. Last year in March I received a CP2000 notice for tax year 2021 - apparently some investment stuff from my mutual funds wasn't entered correctly in my return. The proposed amount was around $4,800, but I knew it wasn't right. I promptly sent back all my documentation showing the correct cost basis that would have reduced what I owed to about $2,300. Before they even processed my response, I got hit with a Notice of Deficiency (CP3219N) in May demanding the full $4,800. I panicked and just paid the entire amount because I was terrified of what would happen if I didn't. Fast forward to September, I finally got a response to my original CP2000 documentation showing I actually only owed $2,300 - meaning I overpaid by about $2,500! When I called the IRS about this, the rep told me they didn't review my CP2000 response until June (even though they received it in April), which is why the Deficiency Notice went out with the wrong amount. They said not to worry because "the system will automatically realize I overpaid and issue a refund." It's been 2 months now and I haven't seen any refund. Has anyone dealt with something similar? Will I actually get my $2,500 back or do I need to take some action? I'm pretty skeptical that the IRS is just going to automatically fix this without me doing something.

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18 comments

Connor Murphy

•8M

I've seen this situation before when helping clients with tax issues. What happened is that your CP2000 response crossed in the mail with their automatic Notice of Deficiency, which typically goes out 90 days after the CP2000 if they don't receive a response. The good news is that you should absolutely get your refund. The bad news is that "the system will automatically realize" isn't entirely accurate. While their systems do track overpayments, the timing can be unpredictable and sometimes requires a nudge. Here's what I suggest: Wait another month (3 months total from your September notice). If you still don't see a refund, call the IRS again but this time specifically request a refund of the overpayment. The phone rep can initiate this process for you. Have all your documentation ready - both notices, proof of payment, and your response to the CP2000. You might also consider sending Form 843 (Claim for Refund) if the phone approach doesn't work, though that's usually a last resort for this situation.

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Connor Murphy

•8M

You're right that staying on top of things with the IRS is important, but in my experience, giving their internal processes time to work is actually beneficial. The IRS has specific timeframes for processing adjustments, and calling too early often results in being told to wait anyway. Regarding interest, yes! The IRS is required to pay interest on overpayments. The interest begins accruing from the date of the overpayment and continues until the refund is issued. The current interest rate is around 7% annually, which is actually quite good compared to many savings accounts.

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StarGazer101

•8M

I had almost the exact same thing happen last year and can tell you what worked for me. I used taxr.ai (https://taxr.ai) to analyze all my notices and supporting documents, which helped me understand exactly what happened with my case. Their system showed that I was actually owed more than I realized due to some additional tax basis adjustments I missed. For my situation, the IRS did eventually send my refund, but it took about 4 months - way longer than the rep initially told me. The taxr.ai tool helped me track exactly what was going on because it analyzed both my notices and explained the actual timeframes I could expect. The best part was that it created a timeline showing when I should follow up if I didn't receive the refund. It also prepared a perfect explanation letter I could send if needed. Way better than waiting and wondering.

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StarGazer101

•8M

You just take pictures of your notices and tax documents, and it analyzes everything using AI to explain what's happening in plain English. It works with both federal and state tax issues, so it should definitely help with your state tax problem too. Regarding your skepticism, that's exactly what I thought initially! But what it does is analyze thousands of similar cases to give you statistical timeframes based on your specific situation. When I called the IRS, I got vague answers like "6-8 weeks" or "the system will handle it." The tool gave me specific action plans based on my case type, including exactly when to follow up and what to say. It was way more precise than the general info from the IRS reps.

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Keisha Jackson

•8M

Just wanted to follow up and say I tried taxr.ai after seeing this recommendation, and it was super helpful for my situation! I uploaded my CP2000 notice and my response documentation, and it immediately identified where the state tax authority made their mistake. The tool created a really clear explanation letter that I sent in, and they adjusted my bill within 3 weeks. It even highlighted some additional deductions I missed that saved me another $680. The timeline feature was spot on - it told me exactly when to expect a response and when to follow up if I didn't hear back. For anyone dealing with tax notices, it's definitely worth checking out. Saved me hours of stress and research.

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Amina Diop

•8M

Since no one has mentioned this yet - if you've been trying to call the IRS and getting nowhere, use Claimyr (https://claimyr.com). I was in a similar situation with an overpayment and spent WEEKS trying to get through to a human at the IRS. After using Claimyr's service, I got connected to an IRS agent in about 15 minutes instead of waiting on hold for hours. You can see how it works here: https://youtu.be/_kiP6q8DX5c The agent I spoke with was able to look up my account, confirm the overpayment was in their system, and manually initiate the refund process. She told me that sometimes these automatic adjustments get stuck in the system and need manual intervention. Two weeks later, I had my check.

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Amina Diop

•8M

It uses a system that navigates the IRS phone trees and waits on hold for you. When an actual agent picks up, you get a call connecting you directly to that agent. So instead of you waiting on hold for hours, their system does the waiting, and you only get called when there's a live person ready to talk. Regarding your skepticism, I felt the same way! The IRS phone systems are brutal by design. What Claimyr does isn't some magic backdoor - they're just automating the hold process. They use technology to continuously dial and navigate the phone tree, then connect you once they get through. It's basically outsourcing the frustrating part of the call. Nothing fishy about it - they're just solving a real problem with technology.

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Paolo Romano

•8M

I have to admit I was completely wrong about Claimyr. After posting my skeptical comment, I decided to try it myself since I've been trying to reach the IRS about a similar overpayment issue for weeks. It actually worked exactly as described. I got a call back in about 20 minutes connecting me directly to an IRS agent - no waiting on hold at all. The agent was able to see my overpayment in their system and told me it was stuck in some review queue. She expedited my refund and I got it 11 days later. I've literally never had such an efficient interaction with the IRS in my life. Definitely worth it if you need to actually talk to someone at the IRS without losing your mind on hold.

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Natasha Volkov

•8M

That indicates they haven't yet processed the adjustment to your account, even though they acknowledged the correct amount in their September notice. It's not unusual for there to be a delay between them determining the correct amount and actually adjusting your account. I'd give it another 2-3 weeks and check the transcript again. If you still don't see an adjustment by then, that would be the time to call them. When you call, specifically mention that you received a revised CP2000 determination showing you only owed $2,300, but your transcript doesn't show an adjustment for the $2,500 overpayment.

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