For 15 years, Michele Beckwith oversaw some of the toughest federal prosecutions in California. She went after transnational terrorists, sex traffickers and the Aryan brotherhood.

She became the acting U.S. attorney in Sacramento this year when her boss, a Biden appointee, stepped down in January.

But her career crumbled in July, she said, after she issued a warning to Gregory Bovino, the California face of President Trump’s immigration crackdown.

The dismissal of Ms. Beckwith appeared to be an early example of how Mr. Trump has fired top federal prosecutors who did not help carry out his political agenda.

Last week, Mr. Trump fired a U.S. attorney in Virginia who determined there was insufficient evidence to indict James B. Comey, the former F.B.I. director, and Letitia James, the New York State attorney general, both political targets of the president. The Virginia prosecutor was replaced by a Trump loyalist who convinced a federal grand jury on Thursday to indict Mr. Comey on two counts.

Documents reviewed by The New York Times show that the July 15 firing of Ms. Beckwith occurred less than six hours after she told Mr. Bovino, the Border Patrol chief in charge of the Southern California raids, that a court order prevented him from arresting people without probable cause in a vast expanse that stretches from the Oregon border to Bakersfield. She was removed not only from her post as acting U.S. attorney in the Eastern District of California, but from the office altogether.