For tax year 2021, file an amended return and pay the 6%
For tax year 2022, file an amended return and pay the 6%
For tax year 2023, file an amended return and pay the 6%. You will need the 2023 form 5329 when you work on 2024.
At this point, you need to make two separate withdrawals. One withdrawal is a normal withdrawal of $6000. No special procedure or special rules. The other withdrawal is the $3000 of 2024 excess contribution plus net attributable earnings.
Then, file an amended 2024 return. You will tell Turbotax that you had a carryover excess of $6000. You will also tell Turbotax that you made a current year (2024) excess contribution of $3000. Turbotax will ask, do you want to remove the excess plus earnings. You will say yes. You will then go to the section for 1099-R income and create a substitute 1099-R that will report the removal of $3000 excess plus earnings. Box 1 is the entire amount of the withdrawal, box 2a is the taxable earnings, and use codes P and J in box 7.
Your final amended 2024 return should include form 5329 that will show the $6000 carry forward excess, plus the 6% penalty, but it will not show the $3000 because that was timely removed. Include “Filed pursuant to section 301.9100-2” as part of the reason for the amended return.
Then, in January 2026 you should get two 1099-Rs from the Roth IRA, one for $6000 with code J or 1J in box 7, and the other for $3000 plus earnings with code PJ. Enter the 1099-R for the $6000, but it will not be taxable since withdrawals of contributions are not taxable. I don;t think you enter the 1099-R for the $3000 (because you entered that on your 2024 return), but even if you did enter it, the code PJ should tell Turbotax that it is not taxable on your 2025 return.
