Does anyone know if tax software like TurboTax automatically calculates the Social Security tax overpayment refund? Or do I need to manually enter something specific?

This is such a relief to read! I'm in almost the exact same boat - left my job in July after hitting the SS tax cap, then started a new position where they've been withholding SS tax for the rest of the year. I've been losing sleep over whether I'd have to deal with separate payments and refunds. Based on what everyone's saying here, it sounds like the IRS will just net everything out on my 1040, which makes way more sense than having to juggle multiple transactions. The safe harbor rule explanation was especially helpful - I definitely paid over 110% of last year's tax through withholding, so that should protect me from penalties. Thanks to everyone who shared their experiences and tools. It's nice to know this is a common situation and there are resources to help navigate it!

I'm in the same boat with TaxAct! One thing nobody mentioned - check your email spam folder. I found an email from the IRS with instructions about my payment plan that got filtered out. It had a link to set up my online account and explained the whole process. Also the letter confirming your payment plan approval (with all the details) comes separately from your tax return confirmation, so watch for that too. Once I got that letter and set up my online account, everything showed up correctly and I could manage my payments there.

Great to see this got resolved! Just wanted to add for anyone else in this situation - if you're still having trouble finding that IRS email or it never came through, you can also call the IRS automated line at 1-800-829-0922 and use the automated system to check your installment agreement status. You'll need your SSN and the exact amount you owe, but it can confirm if your payment plan was approved and when your first payment is due. I had a similar issue where the email never came (even checked spam) and this automated line saved me from waiting on hold. It also gives you the option to speak to a representative if you need to make changes, though as others mentioned, services like Claimyr can help you get through faster if the wait times are crazy.

Protip: Print it out and use different colored highlighters for different codes. Makes it way easier to track whats happening

I feel your pain! When I first got mine I literally stared at it for like an hour wondering if it was written in code 😂 The IRS has a master file transcript guide on their website that breaks down what each code means, but honestly it's still pretty technical. Focus on the "Account Transcript" section first - that's where you'll see your refund status. Look for transaction code 846 with a date - that's when your refund was/will be issued!

Not to be that person but I'm gonna go against what everyone else is saying. DON'T PAY IT YET! Call IRS first. I had literally the same scenario last year. I was about to pay a $750 penalty but talked to the IRS first. They could see my CPA had already filed the abatement and put a 45-day hold on collections activities while they processed it. If you pay now, you might have to wait 6+ months to get that money back, even after the abatement is approved. The IRS is super backed up on processing refunds. Also FYI - the IRS online account system is terrible at showing penalties correctly. Mine showed $0 the entire time too, even though I had multiple notices saying I owed.

I'm dealing with a very similar situation right now! My LLC partnership got hit with a $380 penalty that my accountant said they'd handle with an abatement letter. That was 6 weeks ago and I just got my first collections notice today. Reading through all these responses, I think I'm going to call the IRS first thing Monday morning to see if I can get a collections hold while the abatement processes. If they can't guarantee that, I'll just pay it to be safe. One thing I learned from my research - you can actually check if your CPA really filed the abatement by asking the IRS for a "transcript" of actions taken on your account. They can tell you exactly what correspondence they've received and when. Might be worth asking for that when you call, just to make sure your CPA actually did what they said they'd do. The interest charges are minimal compared to the stress of potential bank levies, especially with your dad's property sale coming up. Better to pay now and get refunded later than risk having accounts frozen during a real estate transaction.

Idk if this helps but I got a letter from Pioneer (another IRS collection agency) last year. Called the IRS directly and found out I qualified for Currently Not Collectible status because of financial hardship. The collection agency never mentioned this was an option even though I told them I couldn't pay. So definitely talk to the IRS directly about ALL your options, not just the ones the collection agency tells you about.

This is really helpful information everyone is sharing! I'm in a similar situation with a late filing penalty for my LLC. One thing I wanted to add - when you call the IRS directly about penalty abatement, make sure you have all your documentation ready. They'll want to know the specific reason for the late filing and any supporting evidence. For health-related issues with your accountant, if you have any documentation of that (like medical records or communication showing the accountant was unavailable), it could strengthen your reasonable cause argument. The IRS is generally pretty understanding about situations beyond your control, especially if you have a good compliance history. Also, when you do call, be prepared to explain why this was a one-time occurrence and what steps you've taken to prevent it from happening again. They like to see that you're being proactive about future compliance.