No, you aren't paying taxes twice.
Tax withheld is just an estimated advance payment of your taxes. The final tax amount can only be determined when you fill out your tax return. If too much tax was withheld, you'll receive a refund; otherwise, there'll be a tax due.
You have to enter that form 1099-R on your tax return.
You can enter your form 1099-R by following these steps:
- In TurboTax, open your tax return
- Click on the down arrow next to Federal in the left-hand column then on Wages & Income
- Locate the section Retirement Plans and Social Security and click on the down arrow on the right
- Click Start next to IRA, 401(k), Pension Plan Withdrawals (1099-R).
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