WASHINGTON—President Trump is replacing the acting IRS commissioner that he appointed just three days earlier, according to people familiar with the matter, making a sudden shift that continues an unusual upheaval at the tax agency.

Gary Shapley, whom President Donald Trump named acting commissioner of the Internal Revenue Service earlier this week with the support of Elon Musk, will no longer serve in the role, sources told CNN — a win for Treasury Secretary Scott Bessent’s office,