Robert Khuzami, the federal prosecutor in Manhattan who supervised the criminal case against President Trump’s former lawyer Michael Cohen, is stepping down from his position next month.

During Mr. Khuzami’s 15-month stint as deputy U.S. attorney for the Southern District of New York, he oversaw one of the most significant investigations in the office’s recent history, securing the guilty plea of Mr. Cohen for eight federal crimes, including two campaign-finance violations tied to hush-money payments he made on Mr. Trump’s behalf during the 2016 presidential campaign.

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The case has exposed Mr. Trump’s inner circle to legal peril and spawned other investigations that will continue after Mr. Khuzami’s departure, including a criminal probe of the donations into and spending of Mr. Trump’s 2017 inauguration. The hush payment investigation also examined the role of executives from the Trump Organization, Mr. Trump’s family business.

Mr. Khuzami oversaw the Cohen investigation after Geoffrey Berman, the appointed U.S. attorney, recused himself for undisclosed reasons.

Under Mr. Khuzami’s supervision, federal prosecutors in Manhattan directly implicated the president in Mr. Cohen’s payoff scheme, referring to him in court papers as “Individual-1.” The prosecutors wrote in a December court filing that Mr. Cohen “acted in coordination with and at the direction of” Mr. Trump in arranging two illegal hush-money payments in 2016 to women who alleged they had sexual encounters with Mr. Trump.

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Mr. Trump has denied the encounters and denied directing his lawyer to break the law.

Mr. Khuzami, whose last day is April 12, will return to Washington to be with his family after commuting weekly to New York, according to an announcement from the Manhattan U.S. attorney’s office.

This story continues in the Wall Street Journal.