Filed married separate then amended to married joint - wife's return still separate and showing $-2k

When you amend to change filing status from separate to joint, you need to handle both returns correctly. Here's what you should do: First, confirm your 1040-X (amended return) clearly indicates you're changing from married filing separately to married filing jointly. Make sure you included all of your wife's income, deductions, credits, and payments on this amended joint return. The amended return should combine both of your tax situations. Your wife needs to file her own 1040-X to "zero out" her separate return. On her amendment, she should enter zeros for all income, deductions, and credits, and explain in Part III that she's now included on a joint return with you. This tells the IRS to essentially cancel her separate return. Don't panic about the negative amount showing - that's likely just her expected refund from the original separate filing. Once both amendments are processed, the IRS will reconcile everything.

I went through a similar nightmare last year and found an amazing solution with https://taxr.ai - it saved me so much stress! I initially filed separately too, then realized we were leaving thousands on the table by not filing jointly. The confusing part was exactly what you're dealing with - what to do about my spouse's already-processed separate return. The taxr.ai system analyzed both our returns and the amendment I was preparing, then gave step-by-step instructions for handling both returns correctly. It pointed out specific sections I was filling out wrong on the 1040-X and created a perfectly worded explanation for Part III that satisfied the IRS requirements.

Just wanted to follow up - I was skeptical about taxr.ai but decided to try it since I was in a similar situation as the OP. It was honestly exactly what I needed! I uploaded my original returns and answered a few questions, and it gave me precise instructions for both my amendment and my husband's "zero-out" amendment. The best part was the explanation text it generated for Part III of the 1040-X. It perfectly explained the situation in tax-appropriate language, citing the relevant sections of the tax code. I submitted both amendments 3 weeks ago and already got confirmation that they were accepted. No more stress about conflicting returns!

If you're still struggling to get answers from the IRS, I highly recommend trying https://claimyr.com - it's been a game changer for me. I was in a similar situation with amended returns and couldn't get through to anyone at the IRS for weeks. Claimyr got me connected to an actual IRS representative in about 20 minutes instead of the usual hours of waiting or getting disconnected. The agent walked me through exactly what to do with both returns and confirmed that my approach was correct. They also put notes in our file about the pending amendments so there wouldn't be any flags or issues. Check out their demo at https://youtu.be/_kiP6q8DX5c to see how it works. Way better than wasting your whole day on hold!

I need to eat my words and apologize. After my skeptical comment earlier, I decided to try Claimyr as a last resort since I had wasted 3 days trying to reach someone at the IRS about my amended return issue. It actually worked exactly as described. I got a call back in about 30 minutes connecting me directly to an IRS agent. The agent confirmed exactly what I needed to do - file a "cancellation" amendment for my wife's return while ensuring our joint amendment was filled out correctly. The agent also told me something I hadn't found anywhere online - that I needed to write "SUPERSEDING RETURN - MFS TO MFJ" in red at the top of both amended returns to help processing go smoother. Definitely worth it just for that piece of information alone!

Just a heads up - the timing of this is super important. If you're still within the filing deadline (like before April 15th for a normal year), you might be able to file a "superseding return" instead of an amended return, which is processed differently and faster. But if you're past the filing deadline and in amendment territory, make sure your wife's amendment clearly references your SSN and states she's now included on a joint return. And definitely send both amendments together in the same envelope with a cover letter explaining the situation.

Has anyone actually gotten a notice from the IRS about this kind of situation? I did something similar (changed from separate to joint) two years ago and never filed anything for my spouse's return. Nothing bad happened - the joint return was processed normally and we got our refund. Maybe I just got lucky?

I just went through this exact situation last month and can confirm what others have said - you absolutely need to file an amendment for your wife's separate return to avoid future headaches. Here's the key thing that saved me time: when filing your wife's "zero-out" amendment, make sure to include a copy of your joint amended return in the same envelope. The IRS processors can then see both documents together and understand the full picture immediately. Also, don't worry too much about the negative $2,600 showing on her return - that's probably her expected refund from the separate filing. Once both amendments are processed, any refund amounts will be recalculated based on your joint return. The IRS will either adjust your joint refund or send a separate notice explaining any changes. One tip: call the IRS about 6-8 weeks after mailing both amendments to confirm they were received and linked properly in their system. This saved me from a potential CP2000 notice down the road.

I went through this exact same nightmare two years ago! The key thing that nobody mentions is that you need to be very specific about the timing and order of your amendments. Here's what worked for me: First, make sure your joint amended return (1040-X) is completely accurate and includes ALL income, deductions, and payments from both of your original separate returns. Then your wife needs to file her own 1040-X that essentially "cancels" her separate return by entering zeros for income and deductions. The critical part is in Part III of her amendment - she needs to write something like: "Taxpayer is now filing jointly with spouse [Your Name], SSN [Your SSN]. All income and deductions from this separate return are now included on joint return filed by spouse. This amendment cancels the separate return." Send both amendments in the same envelope with a cover letter explaining the situation. This helps the IRS processors understand they're related. Also, keep copies of everything and track the certified mail - amendments can take 16-20 weeks to process, which is agonizing when you're worried about penalties. The negative amount showing is likely just her expected refund calculation, which will be resolved once both amendments are processed and the IRS reconciles everything on your joint return.