I paid my IRS tax bill with Direct Pay confirmation but now they claim I still owe them

7 This happens more often than you'd think. Most likely your payment was received but hasn't been properly applied to your account yet. The IRS processing systems can take 2-3 weeks to fully update, and sometimes payments get misapplied or held in suspense accounts. First, print out your Direct Pay confirmation as proof of payment. This will have a confirmation number that's crucial. Next, call the IRS (I know, easier said than done) and explain the situation. Have your confirmation number ready. They can trace your payment using that number. Another possibility is that you made the payment but applied it to the wrong tax year or wrong type of tax. For example, if you applied it to 2023 taxes instead of 2024, or to estimated taxes instead of the tax due with your return.

9 I had a similar issue last year and discovered taxr.ai was super helpful for tracking down what happened with my "missing" payments. I was going crazy trying to figure out where my $3,800 payment went after getting a notice saying I still owed money despite having a confirmation number. I uploaded my Direct Pay confirmation and the notice to https://taxr.ai and their system helped identify that my payment had been applied to the wrong tax year (I had accidentally selected 2022 instead of 2023). They generated a detailed explanation document that I could use when calling the IRS, showing exactly what happened and how to fix it.

19 Just wanted to follow up - I decided to try taxr.ai after my payment issues continued. Uploaded my Direct Pay confirmation and the IRS notice I received. Their system immediately identified that my payment had been processed but was sitting in the IRS suspense account because I had mistyped one digit in my SSN during the payment process! The report showed exactly what happened and gave me specific instructions about what to tell the IRS to resolve it. Called the IRS with this info and got it fixed in one call instead of the three unsuccessful calls I made before. Seriously saved me hours of frustration!

3 If you're having trouble getting through to the IRS on the phone (which is likely), I recommend using Claimyr. I was in a similar situation with a "missing" payment of $4,800 and spent days trying to get through to an agent. I found Claimyr at https://claimyr.com and watched their demo at https://youtu.be/_kiP6q8DX5c. They basically hold your place in the IRS phone queue and call you when an agent is about to answer. Saved me from wasting hours listening to hold music. I got connected to an IRS agent in about 90 minutes (while I was doing other things), explained my situation with the payment confirmation number, and they located my payment which had been applied to my account but hadn't been processed against the specific tax debt yet.

16 I was super skeptical about Claimyr as I mentioned above, but after another failed attempt to reach the IRS (2 hours on hold before being disconnected), I decided to give it a shot. Not gonna lie, I was shocked when I got a call back saying an IRS agent was about to come on the line! Got connected to an actual helpful person who tracked down my payment using my confirmation number. Turns out my $4,400 payment had been received but was applied to my 2022 balance when it should have been for 2023. The agent transferred it to the correct year while I was on the phone. Problem solved in one call instead of weeks of frustration. Should have done this sooner!

5 One thing to check is if the $5,312 they're saying you owe now includes the original amount plus penalties AND interest. The IRS often sends notices that look like duplicate bills but are actually the original amount plus accumulated penalties and interest. For example, if you owed $5,200 originally, the extra $112 could be a failure-to-pay penalty plus interest, and their system might not have registered your payment yet. When did you receive the notice? There's usually a date on the notice itself when it was generated, and if that date is close to when you made your payment, they probably just crossed in the mail.

11 Has anyone noticed that the IRS systems seem worse this year than ever before? I've had multiple issues with payments not being properly credited, and I know several people who've had similar problems. I made a payment in February and it took until May for it to show up in my account!

I've been through this exact situation! The most likely scenario is that your payment was received but hasn't been fully processed yet. The IRS systems can be incredibly slow, especially during busy periods. Here's what I'd recommend: First, make sure you have all your documentation ready - your Direct Pay confirmation number, bank statement showing the payment cleared, and the notice you received. When you call the IRS (and yes, you'll probably need to call), they can use your confirmation number to trace exactly where your payment went. The interest charges from 4/15/2024 to 7/15/2024 suggest this might be related to a prior tax year balance, not your recent payment. Double-check your Direct Pay confirmation to make sure you applied the payment to the correct tax year and tax type. Also, try accessing your IRS online account at different times of day - their systems are often overloaded during peak hours but work better early morning or late evening. If you can get in, you should be able to see a payment history that shows where your $5,200 went. Don't panic - this is fixable, just requires some patience and persistence with the IRS phone system!