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Suppose I choose to make pre-tax payroll contributions to my 401(k) and/or HSA, of an amount that takes up most of my paycheck. I also selected on my W-4 form to make an extra tax withholding per paycheck, of an amount that also takes up most of my paycheck. Obviously, both of these cannot be satisfied at the same time. Which one takes precedence?

Is it going to make as much of the payroll contributions as possible, and tax is only going to be withheld from the remaining amount, even if they don't withhold as much extra taxes as I told them to? Or, will they reduce payroll contributions to such an amount that it would be possible to withhold extra taxes to the amount I chose?

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This is really a question for your employer. If you have designated a certain amount to be withheld for taxes and a certain amount to be contributed to 401(k) and HSA, and those amounts add up to more than your paycheck, something will need to give. But I don’t know whether or not there are specific nationwide standards that are supposed to be applied in these cases, and even if there are, there is no guarantee that your employer would follow them.

If you are in this situation, just ask your employer what they will do. And if you have a preference, then adjust your withholding and/or contribution amounts so that they don’t add up to more than your paycheck.

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You can't pay more taxes than your taxable income, and as 401(k) and HSA contributions are non-taxable, only the remainder is available for tax withholding.

That is also the better solution for you - if processed the other way around, you would owe more taxes, because there is not as much left for tax-free contributions.

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