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The payroll department screwed up at my company and didn't withdraw the final HSA contribution from my check for the purpose of depositing it into my HSA account. Their solution: just deposit into your HSA from your checking account.

This means I will be not gaining the advantage of a withdraw of pre-tax dollars. Is there a way to reconcile this such that I can regain taxes paid after contributing to an HSA from a checking account?

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When you file your taxes, the contribution will count as a deduction, so it is effectively pre-tax (talking about federal income taxes, which is the typical understanding of 'pre-tax').

What it doesn't give you back is the payroll tax you paid on the amount - Social Security 6.2% and Medicare 1.45% - those are gone.

In other words: an HSA contribution through direct payroll deduction into your HSA bypasses federal tax, Social Security, and Medicare contributions - a contribution from you results only in no federal tax. Still, this is normally the biggest part.

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    Make sure that the deposit is assigned to the correct year.
    – mhoran_psprep
    Commented Dec 30, 2020 at 17:52
  • Im a bit confused because you say it is, "a deduction ... effectively pre-tax" but you also say that I wont get back the payroll tax I paid. If the former is true, I would expect that for my 2020 tax returns, I would get a refund for the taxes I paid. If the latter is true, I wouldn't expect to get that back. Sorry, just confused, it seems like conflicting statements from what I understand.
    – 8protons
    Commented Dec 30, 2020 at 17:53
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    @8protons Payroll taxes and income taxes are not the same. They are two separate taxes. If your contribution to your HSA is done through your employer, you save on both, payroll and income taxes. If you make the contribution on your own, outside of your employer, then you only save on income taxes through a tax deduction when you file your taxes.
    – user19035
    Commented Dec 30, 2020 at 18:46
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    @MichaelA that's true in general for why it's better to contribute through your employer. Fortunately in this case it's only the last payment of the year, so maybe only 1/24th ($11) lost because of the mistake. (Even less if paid every 2 weeks, or weekly.)
    – TTT
    Commented Dec 30, 2020 at 23:36
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    @MichaelA , you can try to convince your employer to correct it, but it's work for them. Otherwise, that part is gone-gone. There is no mechanism to get it back except a correction through your employer.
    – Aganju
    Commented Dec 31, 2020 at 0:46

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