How do I enter withdrawals from my retirement accounts by the quarter it was withdrawn?

[Priscilla-nuwash]

For example, I took a specific dollar amount out in each quarter for 2025 without depositing taxes when they were due, so shouldn't the tax penalty be based on the dollar amount each quarter versus a penalty for the whole year as though the entire amount's taxes were due after the first quarter?

[baldietax]

the penalty is calculated on Form 2210, by default based on your safe harbor for the year, less withholding, divided by 4 against each quarterly due date, as you're expecting I think.  To explain why you're seeing a penalty calculated as though that entire amount is due since Q1 you'd need to provide more details.

If you are on desktop you can bring up Form 2210 in Forms mode - it doesn't display by default but do Open Form and type in 2210.  Not sure for TT Online equivalent but I assume it's shown in the PDF with all forms and worksheets.

the safe harbor will be the smaller of 90% of your 2025 tax, or 100% of your 2024 tax (110% if 2024 AGI > 150k or 75k if filing MFS) - see lines 1-9 on Form 2210.

if your quarterly distributions and other income were even throughout the year and you didn't pay withholding or ES then the Annualized Income method probably won't help (and note also for this method the quarters are uneven, ending 3/31, 5/31, 8/31, 12/31), but if your income is back-loaded towards later quarters you may be able to reduce the penalty (once you're comfortable with your original question about that default calculation to begin with).  You can work thru this under Other Tax Situations / Underpayment Penalty section.

[MaxA1]

You can only enter your retirement distributions for the year.  You can't enter it by quarter.  TurboTax will ask you how the distributions were made shortly after you enter the information on your 1099-R.  That is where you can show that you received period payments.  Revisit the 1099-R section in the Wages and Income section and work through the questions again to clarify how the distributions were made.  Consider also going to the Other tax situations section and visit the underpayment penalties section to answer questions regarding your estimated tax penalty calculation.