The Trump administration has turned campaign promises to target universities into devastating action, pulling hundreds of millions in federal funds from Columbia University and the University of Pennsylvania.

On Monday, the Trump administration went after Harvard, the world’s wealthiest university, announcing that it would review about $9 billion in contracts and multiyear grants. It accused the university of failing to protect Jewish students and promoting “divisive ideologies over free inquiry.”

Harvard had been bracing for the development. In recent months, it had moved cautiously, seeking compromise and, critics said, cracking down on speech. The approach riled some who worried that Harvard was capitulating at a moment of creeping authoritarianism.

Though it remains unclear how much the university will actually lose, if anything, the move on Monday shows that the conciliatory approach hasn’t fended off its critics yet.

In the days leading up to the Trump administration’s announcement, faculty members called on the university instead to more forcefully defend itself and higher education more broadly. In a letter, more than 700 faculty members called for Harvard to “mount a coordinated opposition to these anti-democratic attacks.”

“As much as a body blow from the administration would hurt us, Harvard has the capacity to withstand the blow,” said Steven Levitsky, a Harvard political science professor who circulated the letter.

But a lot of money could be in question, and the stakes at Harvard underscore the excruciating dilemma faced by leading universities and civic institutions, from law firms to nonprofits: Should they work to protect themselves, as many seem to be doing, or stand on principle?

“That every-man-for-themselves response is about to cost us our democracy,” said Dr. Levitsky, who studies authoritarian regimes.

As President Trump’s inauguration approached, Harvard hired Ballard Partners, a lobbying firm with deep ties to Mr. Trump. On the first full day of the Trump presidency, the university announced it was adopting a highly debated definition of antisemitism — which labels certain criticisms of Israel, such as calling its existence racist, as antisemitic — a move encouraged by the new administration but slammed by free speech advocates.

As the spring went on, pro-Palestinian actions spurred campuswide messages, even as Harvard remained quiet when a former Israeli prime minister visited and joked about giving student hecklers pagers, said Ryan Enos, a Harvard political science professor. (The comment was an apparent reference to the exploding pagers Israel used to target Hezbollah last fall.)

Under pressure, Harvard recently suspended a partnership with a Palestinian university while agreeing to start a new partnership with an Israeli one.

Then last week, two leaders of Harvard’s Center for Middle Eastern Studies were pushed out of their positions after a Jewish alumni group complained about programming, according to faculty members. To some faculty members, the move was more evidence that Harvard was capitulating at a moment of creeping authoritarianism.

“It’s pretty transparent what’s going on,” Dr. Enos said. “Harvard is trying to put on a posture that mollifies its critics.”

Many say Harvard’s actions make sense, given the money at stake. And to many on the right and even some on the left, Harvard’s recent actions are a correction.

Harvard has often been criticized by conservatives who say that left-leaning politics permeate the campus and make it hard for different views to be heard. For years, it has also become a target for conservatives who say efforts to make higher education more inclusive of racial minorities have been excessive. Harvard, along with the University of North Carolina, was drawn into a Supreme Court case over its consideration of race in admissions, for instance. It ultimately lost in the conservative-leaning court, leading to a national ban on race-conscious admissions.

Last year, amid pressure, Harvard’s largest division ended a requirement that job candidates submit statements about how they would contribute to diversity.

As the war in Gaza set off student protests and debate over university responses, some have pushed for the federal government to use its power, and its purse strings, to force additional change.

Others, like Jeffrey Flier, the former dean of the Harvard Medical School, have called the Trump administration’s attack on higher education “an existential threat.” But Dr. Flier said the assault was occurring in part because of higher education’s failure to take seriously the free expression concerns of conservatives and even political moderates.

He said that Harvard and other universities had tolerated behavior toward Jewish students that they would not have if it had been directed at other minorities and had generally created an unhealthy environment for the expression of heterodox views. Dr. Flier said Harvard had begun to address some of those issues — moving away from commenting on political issues, for example — before Mr. Trump took office.

“We were beginning to go in the right direction,” Dr. Flier said. “There was a vibe shift. And an awareness shift. And that all got shifted again by the Trump administration’s massive, uncalled-for, pretextual attacks.”

Bowing to federal pressure has not proved to be a solution, either.

Last week, Columbia’s interim president resigned — the second leader there to do so in a year — amid intense internal and external pressure over the Trump administration’s demands on the university.

Dylan Saba, a lawyer with Palestine Legal, noted that Columbia had fallen in line with many Republican demands before Mr. Trump took office and had taken an especially aggressive stance against pro-Palestinian activists, including denouncing scholars by name at a congressional hearing. It did not placate Mr. Trump and produced even more student activism, Mr. Saba said.

“In seeking a painless way out, they ended up producing a much bigger conflict,” he said.

Amid the speed and chaos of Mr. Trump’s assault on higher education, colleges have not figured out how to respond in a way that will satisfy their antagonists — if there is one. Some faculty members wonder whether the conciliatory approach has only emboldened critics.

Even for universities with sizable endowments, the financial hits the administration has promised could be painful. Harvard’s endowment is more than $50 billion. Johns Hopkins University, which also has a large endowment, recently announced it would cut more than 2,000 employees because of reduced federal funding.

Harvard did not respond to a request for comment. Earlier this spring, Alan Garber, Harvard’s president, wrote in communication to the campus that community members should “rest assured that Harvard is working hard to advocate for higher education in our nation’s capital and beyond.”

Harvard has been a longtime target of Republicans who want to take it down a notch. In the days after the Oct. 7 Hamas attack on Israel, which killed 1,200 people, student groups released a statement holding Israel responsible for the assault. In response, Harvard’s president at the time, Claudine Gay, released a tepid statement denouncing the attack.

Amid pressure, she followed it with a stronger message, but Harvard was one of three colleges whose leaders were questioned by Congress in 2023 about their efforts to combat antisemitism. A month after a widely panned performance, Dr. Gay was out.

Ongoing protests, unrest and lawsuits have kept Harvard in the public eye, though they have quieted considerably since last spring. In the fall, pro-Palestinian demonstrators staged a silent “study-in” in a library, and the university temporarily banned them from the space.

In lawsuits over the last year, Jewish students said that Harvard had allowed hatred and discrimination to go unchecked and that it still had a long way to go to fix endemic problems. They accused Harvard of ignoring antisemitism, by allowing chants like “from the river to the sea” and the showing of the film “Israelism,” a documentary critical of Israel.

This winter, Harvard was placed on a list of 10 universities the Trump administration was taking special interest in.

“The sharks circle when they smell blood in the water,” said Kenneth Roth, a former director of Human Rights Watch and a fellow at Harvard, who wants Harvard to fight better to allow robust debate and academic freedom.

The announcement on Monday did not make it clear what other steps the university would have to take to be in good standing with the federal government.

Some universities have been more vocal amid the federal onslaught. A Georgetown law dean responded forcefully earlier last month to Washington’s top prosecutor, a Trump loyalist, saying his efforts to control the university’s curriculum were unconstitutional. Brown’s president wrote recently that it would defend its academic freedom in the courts, if need be. And Princeton’s president recently condemned the attack on Columbia, calling it “the greatest threat to American universities since the Red Scare of the 1950s.”

Other universities also appear to be taking a more cautious approach.

Last month, the University of California system announced it would end the use of diversity statements in hiring — a practice that had been under fire from conservatives for years. Michael V. Drake, the president, had told faculty leaders he didn’t want the system to be “the tallest nail” and stand out, according to Sean Malloy, a professor who was in the meeting. A spokesman for the system said the meeting was meant to be confidential, and that Dr. Drake was relaying a sentiment he had heard on a trip to Washington.

And Dartmouth College recently hired a former chief counsel for the Republican National Committee as its vice president and general counsel, to help “understand and navigate the legal landscape surrounding higher education,” President Sian Leah Beilock said in a statement.

Noah Feldman, a Harvard law professor, said it was only rational for Harvard, or any university, to try to negotiate a solution with the Trump administration, given the arbitrary nature of Mr. Trump’s actions against higher education and the number of jobs on the line.

Professor Feldman, who has criticized Mr. Trump’s actions, said Harvard had acted responsibly, given the political climate.

“Sometimes people who are eager for the university to get up and make big statements have a slightly unrealistic conception of what the real-world effect of those statements would be,” he said.