Retirement tax questions

Check your safe harbor calc - see Form 2210 line 1-9, to avoid penalty you need to have paid during the year via withholding or "timely" estimated taxes, the smaller of 100% of your 2024 tax (110% if AGI > 150k of 75 if filing MFS), or 90% of your 2025 tax.

Withholding is always considered timely regardless of when it happens, but given you did a large Roth last year also it sounds like W2 withholding alone will not meet the safe harbor.

For a large Q4 Roth conversion, you would likely need to make a Q4 estimated tax payment in January to meet the safe harbor amount (which may not be the full 24% tax due on the conversion - the rest is due by next April), and then when you file your return will need to adopt the Annualized Income method on Form 2210.  Without that method by default, IRS (and TT penalty calc) will assume this distribution happened evenly thru the year and you were therefore underpaid in Q1-3 etc which is why you got the large penalty.  For the AI method you will need to calculate your AGI, withholding, Qualified Divs, LTCG etc by quarter (not even quarters tho  - 3/31, 5/31, 8/31, 12/31) and that will show the uneven income in those buckets and that the estimated tax in Q4 was not late.  It may not entirely eliminate the penalty if other things didn't quite line up but should significantly reduce it.  When you do your 2025 filing you would trigger this process under Other Tax Situations / Underpayment Penalty section and check the outcome on your 1040 Line 38.  But beware these quarterly calculations you need to do yourself and input into Turbo.  You would need to do a similar process for your state taxes also if applicable.

There is an alternative approach where you can do withholding on the Roth conversion which will reduce the amount deposited into your Roth (e.g. 80k comes out of your Trad IRA, 20k withheld, 60k goes into the Roth), which is taking money from your retirement accounts - but you can then send in that amount directly within 60 days to make it up.  I've not tried that method and don't know what's involved with your brokerage to process that deposit into the Roth correctly and not be coded as a contribution - perhaps @VolvoGirl can elaborate if questions on this approach.

Going forward if you're continuing to do these conversions annually, the easiest way is to figure your safe harbor in Q1 when you file for prior year, based on known prior year tax along with estimate of your withholding, and pay even quarterly ES payments thru the year to meet that.  You can then just do your Roth conversion whenever during the year or even in pieces, it doesn't matter.  When you do your 2025 filing, the ES vouchers for 2026 generated by TurboTax will do this calculation by default, using 100/110% of your 2025 tax as the safe harbor and assuming your 2026 withholding is the same as 2025, and the difference between the two is your estimated tax and divide by 4 for the quarterly amount.  You can update these assumptions under Other Tax Situations / Form W4 and Estimated Tax section and see if you can optimize the ES payments further.

Finally try to avoid sending checks and using 1040-ES vouchers, pay ES directly electronically at irs.gov (I do the same with final tax due - tell Turbo you're sending a check rather than give direct debit details, and then pay directly at irs.gov when you want, it's easier to control timing especially for large amounts due - IRS will hit your account by next business day).

Check into the details of the safe harbor, penalty calls and AI method on Form 2210 for more details.