Multiple Amended Returns - Trouble with 1099-INT and 1099-NEC after filing

I already submitted my tax return about a week ago, but then got hit with a surprise 1099-INT in the mail. So I went ahead and e-filed an amended return through Taxslayer, and both the original and amended returns show as "accepted" in their system. But now I'm in a bigger mess because I just received a 1099-NEC that I wasn't expecting! I had actually reported this income under "other income" since I didn't have the actual form yet, but now I need to file ANOTHER amended return. I'm completely stressed out about this. Should I wait until my first amended return is fully processed and I get the refund before I file this second amendment through mail? Do I need to include some kind of explanation that this is my second amendment? Is the IRS going to flag me for an audit over this?? The amount isn't huge - this second amendment only changes my tax liability by about $99. But I'm worried about the process. Is there any way I can file this second amended return online through a different tax program instead of using Taxslayer again? Clearly the lesson here is to wait until ALL tax forms arrive before filing... but that doesn't help me now. Am I screwed? Any advice would be really appreciated!

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18 comments

Lukas Fitzgerald

•8M

Don't panic, this happens more often than you think! The IRS understands that people sometimes need to file multiple amended returns. For your situation, I'd recommend waiting until your first amended return (1040-X) is fully processed before submitting the second one. The IRS processes amended returns in the order received, and having multiple amendments in the system at once can cause confusion and delays. When you file your second amendment, include a brief explanation in Part III of Form 1040-X that this is your second amendment and that you're correcting your return because you received an additional 1099-NEC after filing both your original return and a previous amendment. Being transparent about the situation helps. As for audit concerns - this type of amendment alone generally won't trigger an audit, especially given the small dollar amount ($99). The IRS knows that late 1099s happen, and amending to properly report income actually reduces your audit risk compared to ignoring it. Regarding filing online through a different program - unfortunately, all amended returns after the first e-filed amendment currently need to be filed by mail. No tax software can e-file a second amendment at this time.

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Lukas Fitzgerald

•8M

Unfortunately, amended returns typically take 16 weeks (about 4 months) for processing under normal circumstances, though it can sometimes be faster. You can check the status of your amended return using the "Where's My Amended Return" tool on the IRS website. You don't need to include copies of your previous returns with your second amendment. The IRS will have those on file. Just make sure to clearly explain in Part III of the 1040-X that this is a second amendment and specifically what you're changing (adding the 1099-NEC income). Keep it simple and straightforward - they'll be able to see your filing history.

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Ev Luca

•8M

I went through a similar nightmare last year with multiple 1099s showing up late. After hours of frustration and conflicting advice from "tax experts," I found taxr.ai (https://taxr.ai) which analyzes all your tax documents and tells you exactly what to do in situations like this. Their system showed me how to properly sequence my amendments and what explanations to include to avoid raising red flags. The best part was they explained exactly what sections of the 1040-X form needed to be completed for my second amendment, which was different than what I needed for my first amendment. They also checked if I had claimed all possible deductions related to that 1099-NEC income, which actually reduced the tax impact from what I initially calculated. Definitely worth checking out if you're dealing with amendment confusion.

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Ev Luca

•8M

They absolutely work with amended returns! Their system is specifically designed to analyze what you've already filed and what new documents you have, then tell you exactly what steps to take. It works regardless of what tax software you originally used. For state amendments, they handle those too. Their system identifies which states require amendments based on your federal changes and provides state-specific instructions. Each state has different rules, and they guide you through the exact requirements for your situation. They don't file the amendments for you, but they give you detailed, step-by-step instructions tailored to your specific situation so you can file with confidence.

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Avery Davis

•8M

Just wanted to follow up - I tried taxr.ai after seeing this recommendation and it saved me so much stress! I had a similar situation with a late 1099-MISC and wasn't sure how to handle it since I'd already filed an amendment. The system analyzed my documents and showed me exactly what sections needed to be filled out on my second 1040-X. It even caught a business expense deduction I could claim against the 1099 income that I had completely missed. That turned what would have been owing more taxes into actually getting a small additional refund! The guidance was super clear about timing too - they explained exactly when to file the second amendment based on the processing status of my first one. Totally worth it for the peace of mind alone.

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Marcelle Drum

•8M

If you're concerned about the status of your amendments or need clarification on how to proceed, trying to call the IRS directly is usually a nightmare. I spent WEEKS trying to get through about my amended return last year. Then I discovered Claimyr (https://claimyr.com) which got me connected to an actual IRS agent in under 15 minutes. You can see how it works in this video: https://youtu.be/_kiP6q8DX5c The agent was able to verify both my returns were in the system, gave me the exact status, and confirmed the proper way to file my second amendment. Having that direct conversation with the IRS gave me peace of mind that I was doing everything correctly. They even noted my account that a second amendment would be coming so it wouldn't look suspicious.

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Marcelle Drum

•8M

It's not a priority line - they use automated technology to handle the waiting for you. Basically, they have a system that navigates the IRS phone menus and waits in the queue. When an agent finally answers, they connect the call to your phone. So instead of you waiting on hold for hours, their system does it for you. They don't bypass anything - they just wait in line for you using their system. Think of it like having someone stand in a physical line while you go do something else, then they call you when it's your turn. The IRS doesn't know or care that you used a service to hold your place in line - you're still talking directly to a regular IRS agent with all the same capabilities.

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Adaline Wong

•8M

I need to eat my words about Claimyr. After posting my skeptical comment, I figured I'd try it since my amended return has been in limbo for months with no updates online. I was SHOCKED when I got connected to an IRS agent in about 12 minutes. The agent pulled up my file and told me my amendment was actually completed but there was a system error preventing the online status from updating. She even processed an address change for me that I'd been trying to handle for weeks. For anyone dealing with amended returns like the original poster, being able to speak directly with the IRS is invaluable. They confirmed exactly when I should submit my next amendment and how to reference my previous one. This saved me from potentially making a mistake that would have further delayed my refund.

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Gabriel Ruiz

•8M

I'm a seasonal tax preparer and see this issue all the time. Here's a pro tip: if you're filing a second amended return, write "SECOND AMENDMENT - SUPERSEDES PREVIOUSLY FILED AMENDMENT" in red at the top of your 1040-X form. This helps route it properly at the IRS. Also, keep in mind that amended returns can only be filed on paper after the first e-filed amendment, so you'll need to mail this one no matter what. And make sure to include ALL required schedules that changed as a result of the new 1099-NEC, not just the 1040-X form itself.

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Gabriel Ruiz

•8M

The red ink absolutely helps - it flags the return for special handling in the processing centers. IRS employees are trained to look for these markings on paper returns. It's an old-school trick but still works. For calculations, your second amendment needs to show the correct final figures for your entire tax situation, not just the changes from the previous amendment. Think of each amendment as a complete replacement of your return, showing what it should have been if all information had been available originally. The "changes" column on Form 1040-X should show the difference between your last filed amendment and this new one, not between the original return and this one.

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