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You can eventually get the taxes back, though it might take a while.

Your former employer should take care of the FICA part after you repay them. For federal income tax, you'll claim a tax credit when you file your return according to "Repayment over $3,000" under IRS Pub 525. State income tax may have a similar process, though it can vary depending on the state.

https://www.irs.gov/publications/p525#en_US_2022_publink1000...

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Learned something new, thanks!

In my specific case they sent over an amount to repay that was higher than what I calculated from my original contract, I asked for an itemized breakdown (the original communication just had a single flat number), and I never heard from them again. It was probably more expensive for their lawyers to double check the numbers than the amount they would have received from me.

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