In the past I have taken QCD's from my traditional IRA. Turbo Tax handled this in a straightforward manner. I entered the taxable amount during the interview process, and it was reflected to the 1040 correctly., For 2025, the process appeared to be the same, but the 1040 shows the entire distribution as taxable - it does not show the actual taxable amount, which is the gross distribution less the QCD's I took, which is what I entered in the interview form. When I look at the 1099-R in the Forms mode it shows both the gross distribution and the taxable amount that I entered. What's going on?
Did you look at the actual 1040 or 1040SR line 4a and 4b? If you are looking at a summary screen or review screen those show the full amount as income and lump a lot of stuff together. You need to check the actual 1040 form and make sure it’s right.
It should be the same as last year. When you entered the 1099R did you keep going? There will be a page that asks Do any of these situations apply? Midway down is Were any of these funds sent directly to a charity? Then it will ask for the amount.
The code in box 7 of form 1099-R must be 7 (or new code Y) and the little IRA/SEP/SIMPLE box must be checked.