This is my first time to file form 8606 for the non-deductible IRA. How do I submit the IRA contribution from Form 5498, and will form 8606 automatically populate? Thank you for your assistance.
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In order to direct contributions to be non-deductible and populate Form 8606, you need to indicate this in the IRA entry screen.
Here's how to do this in TurboTax Online:

In order to direct contributions to be non-deductible and populate Form 8606, you need to indicate this in the IRA entry screen.
Here's how to do this in TurboTax Online:

What about if I am using Turbo Tax Premier? I tried the steps you suggested for On-line, and I didn't get the same screens.
The screen will be the same in TurboTax Online if your IRA contributions are deductible, you get the option to make it nondeductible as MindyB shared above. But if you have a retirement plan at work and are over the income limit it will be nondeductible automatically. You will only get a warning that your income is too high to deduct the Traditional IRA contribution and then a screen saying $0 is deductible. Therefore, you will not see the “Choose Not to Deduct IRA Contributions” screen.
I am using TurboTax premier 2025 desktop and I am having a similar issue.
I fill in the maximum contribution for my IRA which is non-deductible, I don't get a screen that asks me to make it non-deductible, and then it says I need to withdraw it at the final screen, charges me a tax penalty, and puts it in form 5329-T as an overcontribution. I've deleted it and tried again but it doesn't work. Is there a bug in the desktop version?
The software works fine. It seems like you made an excess contribution if you are charged the 6% penalty. Please verify that you have taxable compensation to make the IRA contribution.
If you do have an excess contribution then you need to remove the excess plus earnings by the due date to avoid the 6% penalty. Please make sure you request the withdrawal of excess contribution plus earnings with your financial institution. The earnings will be taxable in the year the contribution was made.
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