As the fall semester began at New College of Florida, a small public school known as proudly unconventional until Gov. Ron DeSantis set about overhauling it this year, new students were easy to spot.

Many were recruited athletes, clad in T-shirts branded with the school’s new mascot, a muscled, flexing banyan tree. They stood out from returning students, many of whom roamed the campus in bare feet or with vividly dyed hair.

“Will these people be OK with us being weird as we are?” said Emma Curtis, a 21-year-old fourth-year student, voicing a concern shared by others.

The influx of athletes is just one of the sweeping changes that have come to New College since Mr. DeSantis and his allies vowed in January to transform the liberal arts institution, known as Florida’s “public honors college,” into a bastion of conservatism. More than a third of last year’s faculty members — about three dozen — are gone. So are about 125 students who chose not to return.

In a school that last year had about 700 students total, the freshman class of 338 is the largest ever; it also has a higher proportion of Black, Hispanic and male students than previous ones did, according to the administration. More than 200 students have been moved from on-campus dorms to off-campus hotels to make room for the recruited athletes and other new students.

The pronounced change in climate has led to a flurry of legal challenges. Alumni, faculty and students have sued, claiming free-speech violations that they say amount to academic censorship. The U.S. Department of Education is investigating a complaint that New College, in its new iteration, discriminated based on disability. An alumna accused the new leadership in a separate federal complaint of discriminating against L.G.B.T.Q. students by creating a hostile environment that drove some of them out.

The board of trustees, controlled by DeSantis allies, and the interim president, Richard Corcoran, dismiss the critics as a disgruntled few and cast the overhaul as a success. State lawmakers sent about $50 million to the school this year, a big jump from recent years. New students were offered newly designated scholarships and laptops. Moldy dorms were shut down. And the school created an athletic department, with plans to field six teams.

“What was really missing more than anything else at New College was leadership,” Mr. Corcoran, a former Florida House speaker and state education commissioner, said in an interview. “We’ve been able to do something that wasn’t accomplished in 63 years at the college, and that was grow enrollment. We did it at a time of complete upheaval and negative publicity.”

Much of Mr. DeSantis’s criticism of New College before the overhaul centered on what he characterized as “woke indoctrination” on college campuses. One of the new leadership’s first acts was eliminating the college’s diversity office; soon after, the diversity chief and the academic librarian, both members of the L.G.B.T.Q. community, were fired.

The board of trustees’s faculty representative quit after five professors were denied tenure because of what Mr. Corcoran called a move toward “a more traditional liberal arts institution.” Some new administrators hired into top posts did not have a background in academia, but rather connections to Republican state politics.

“The board wasn’t looking for reasonable change at a reasonable pace,” said Matthew Lepinski, the computer science professor who resigned from the board and then from the school. “They were interested in making change so fast that they didn’t care what they broke.”

The reconfigured board voted to abolish New College’s gender studies program, which one trustee called “more of an ideological movement” than an academic discipline. The school’s only full-time gender studies professor quit, writing in his resignation letter that Florida was “the state where learning goes to die.”

Gone are gender-neutral bathrooms, hallway art that in some cases featured nudity and student murals that had been completed in February and were expected to remain for several years. Student orientation leaders had to remove Black Lives Matter and Pride pins from their polo shirts. A student government election this week pitted a returning student against a new student backed by a newly formed campus chapter of the conservative organization Turning Point USA.

Dan Duprez, a former New College admissions officer, said he was troubled by the tactics used to grow the incoming class, noting that the grade-point averages and standardized test scores of new students were lower than those of past freshman classes. He recalled a colleague showing him an admissions essay that was a screenshot of cellphone notes, “riddled with incorrect spelling and grammar, saying, basically, ‘I just want to play ball.’”

“That person went on to be accepted,” Mr. Duprez said.

Administrators say they had little time to recruit the large incoming class that they wanted. Many top athletes had already committed to other schools, and critics say New College recruited students heavily from Christian schools. Mr. DeSantis has said he wants New College to model itself after Hillsdale College, a private Christian institution in Michigan.

Mariano Jimenez Jr., the athletic director and baseball coach, who used to work at a private Christian high school, said the school brought in academic counselors to keep athletes on track, as other schools routinely do: “We’re going to show that these athletes are going to be held to a high standard.”

Several athletes declined to speak to a reporter. The college declined a request to make athletes available for interviews.

One who did agree to a brief interview, Tyrone Smith, a 20-year-old basketball player, said he transferred from the University of South Florida in part because of New College’s academics. “The professors know your name,” he said.

Friction over the athletes’ arrival grew after many of them were assigned to apartment-style dorms, displacing more senior students. Other dorms were deemed unsafe because of mold, which Mr. Corcoran said should have been addressed by earlier administrations. Many students ended up in three nearby hotels.

Atticus Dickson, a 19-year-old religious studies student assigned to live at a Hyatt Place, described the inconvenience of having to catch a shuttle or hitch a ride just to get to class: “My job is on campus, and I stay on campus late.”

There have been other sources of uncertainty. Annie Dong, a 21-year-old art and psychology student in her fourth year, said the culture no longer felt as positive and welcoming.

“The community has changed,” she said. “There is also anxiety just being on campus.”

Parents and students reported classes being canceled shortly before the start of the semester, a claim Mr. Corcoran denied despite the faculty upheaval. Visiting faculty have been hired for this school year.

“I was doing an internship at an organic chemistry lab,” said Olivia Pare, a 20-year-old biology student entering her third year, who transferred. “The professor I was doing that with was denied tenure, and that was the last straw for me.”

More than 30 students have transferred to Hampshire College, a private liberal arts school in Amherst, Mass., that offered to match New College students’ tuition.

One of them, Libby Harrity, 20, withdrew from New College as part of a deal for misdemeanor battery charges against her to be dropped. Christopher Rufo, a trustee appointed by Mr. DeSantis, had accused her of spitting at him during a campus protest in May. (Ms. Harrity denied his version of events.)

Ms. Harrity — who got a tattoo of New College’s quirky former mascot, a pair of empty brackets denoting a math concept known as the null set — said that she is grateful for Hampshire’s tuition match, though her housing and travel home will be more expensive.

“I’m hurt,” she said of her departure from New College. “They have come in and taken everything that made it good and charming and removed as much of it as possible.”

Ms. Curtis, an art and psychology student, stayed at New College, though she is considering dropping her psychology concentration. The dorm she expected to live in was closed, leaving her to scramble for alternative on-campus housing. She was one of six students whose murals — hers depicted sandhill cranes — were painted over without notice, which she said sent a painful message: “‘We don’t want your work here.’”

She let her pink hair dye fade and her mullet grow out before returning to school — for fear, she said, that administrators and new students would judge her. She is trying to get through her art coursework and graduate as soon as possible.