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 appears to be another example of how Mr. Trump has fired top federal prosecutors who did not help carry out his political agenda.

Her ouster came weeks before 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.

“It’s unjust,” she said of the firings across the federal government this year, in an interview. “We have to stand up and insist the laws be followed.”

Ms. Beckwith, a Democrat, was replaced temporarily by Kimberly Sanchez, a Republican who also worked in the Eastern District. Two days later, Mr. Bovino and his agents went to Sacramento and raided a Home Depot parking lot, where they said they arrested at least eight people for being in the country without authorization.

“Folks, there is no such thing as a sanctuary city,” Mr. Bovino said in a video he shared on social media, with a holstered gun at his hip and canisters secured to his vest as he stood in front of the State Capitol.

“Whether it’s here in Sacramento or nationwide,” he continued, “we’re here, and we’re not going anywhere.”

The end of Ms. Beckwith’s federal career was precipitated by a phone call from Mr. Bovino on July 14. He told her that he was bringing his officers to Sacramento, about 600 miles north of the Mexico border, and wanted to know whom to notify in her office if they were assaulted, she recalled.

Ms. Beckwith said she reminded him that the Border Patrol was under a federal court order prohibiting it from stopping people indiscriminately in her district. It was clear, she said, that he knew about the order but did not seem to think it would stop his raid.

At 10:57 the next morning, she emailed Mr. Bovino to reiterate she expected “compliance with court orders and the Constitution.”

Hours later, her work cellphone went dark. Then her computer did, too. She checked her personal email account.

At 4:31 p.m., she received an email from Saurabh Sharma, special assistant to Mr. Trump.

“Michele,” it stated, “On behalf of President Donald J. Trump, I am writing to inform you that your position as First Assistant United States Attorney and employment with the Department of Justice is terminated, effective immediately.”

Ms. Beckwith was promptly marched out of the office.

A spokeswoman for Mr. Trump referred questions to the Department of Justice, which declined to comment on the matter.

A Department of Homeland Security official, who was part of the Sacramento operation and spoke on the condition of anonymity because they were not authorized to speak publicly, said that federal officials were offended by Ms. Beckwith’s suggestion that immigration agents were going to violate the rights of migrants.

What’s more, the official said, Mr. Bovino felt Ms. Beckwith was refusing to provide his team the legal support it needed to safely conduct the operations.

In a statement, Mr. Bovino said, “The former Acting US Attorney’s email suggesting that the United States Border Patrol does not ALWAYS abide by the Constitution revealed a bias against law enforcement.”

Ms. Beckwith’s impasse with Mr. Bovino was rooted in a lawsuit filed by the American Civil Liberties Union after his border agents conducted the unannounced raids in Bakersfield, where they arrested day laborers outside a Home Depot and farmworkers in orchards in January.

A federal judge in April ruled that the Border Patrol could detain people only if they had a reasonable suspicion that they were violating federal immigration law.

“You just can’t walk up to people with brown skin and say, ‘Give me your papers,’” U.S. District Court Judge Jennifer Thurston said. She granted an injunction stopping the Border Patrol from detaining people without probable cause while the case proceeds.

But that order did not apply to Southern California, where federal officials intensified their crackdown in June, leading to protests and Mr. Trump’s deployment of the National Guard against the wishes of California leaders. A Los Angeles judge in July also placed restrictions on immigration raids in Southern California, but the Supreme Court overruled her decision this month.

“The Supreme Court’s decision is evidence of the fact Border Patrol follows the Constitution and the Fourth Amendment,” Mr. Bovino said.

There are 93 U.S. attorneys overseeing federal prosecutions in districts throughout the country. It is common for them, as appointees, to resign after a new president is elected.

It is not common, however, for presidents to demand that prosecutors carry out certain acts as a condition of employment, said Nina Mendelson, a professor of law at the University of Michigan with expertise in administrative law. U.S. attorneys are supposed to be able to operate freely from political pressure.

“We still have a norm of prosecutorial independence and even-handedness and integrity at the federal level,” she said. “Political pressure to prosecute enemies or shield friends would not typically be considered cause for removal.”

In August, Attorney General Pam Bondi appointed Eric Grant, who defended the Trump administration against major environmental lawsuits during the president’s first term, as interim U.S. attorney for the Eastern District of California. Mr. Grant replaced Ms. Sanchez, who is now second in command in the office, the position that Ms. Beckwith once had.

Ms. Mendelson said the firing of longtime civil servants without cause, as in the case of Ms. Beckwith, is rare. Ms. Beckwith said that while the president had the right to remove her as acting U.S. attorney, he should have allowed her to return to prosecutorial work in the Eastern District.

Ms. Beckwith has appealed her termination, arguing she could not be fired without cause and without due process. She is seeking that her removal be expunged from her record, as well as back pay with interest and attorneys’ fees.

Ms. Beckwith said she was motivated by justice, not politics.

She was raised in Ohio by a father who worked in a fiberglass factory and a mother who stayed home to take care of her and her sister. They did not talk about politics.

She and her husband, also a lawyer, moved to California in 2004 for work and eventually decided to raise their family in Davis, a college town west of Sacramento, where she is a member of the school P.T.A. Though she is a registered Democrat, she pointed out that she has served Republican and Democratic presidents alike.

“I’m an American who cares about her country,” she said. “I’m a public servant. That is my calling.”