About 150 demonstrators affiliated with a progressive Jewish activist group packed into the lower level of Trump Tower Thursday to protest the arrest of Mahmoud Khalil, a Palestinian activist and former Columbia University student.

President Trump has heralded the arrest as his administration moves to deport Mr. Khalil, a legal permanent resident of the United States who was a prominent figure in pro-Palestinian demonstrations on Columbia’s campus.

The protesters held aloft cloth banners printed in red and black lettering. One read: “Free Mahmoud, Free Palestine.” They chanted, their words reverberating against the coral marble tiling. “Fight Nazis, not students,” they repeated.

Ninety-eight of the protesters were later arrested, according to John Chell, the Police Department’s chief of department.

Since news of Mr. Khalil’s arrest on Saturday became public, New Yorkers have taken to the streets, marching in Lower Manhattan and gathering on Columbia’s campus uptown. Free speech advocates and immigrant rights groups have questioned the legality of arresting Mr. Khalil, 30, who has a green card, was born and raised in Syria and is married to an American citizen. His lawyers are challenging his arrest in court.

Shortly before noon on Thursday, hundreds of people who had slowly been streaming into the lower level plaza of Trump Tower, Mr. Trump’s high-rise in Midtown Manhattan, took off their coats and revealed bright red T-shirts that said “Not in Our Name” on the front and “Jews Say Stop Arming Israel” on the back.

In 2015, Mr. Trump launched his first winning presidential campaign from a lectern in the very same building, after descending the golden escalator into the lobby. One of the protesters, Josh Dubnau, said the symbolism was intentional.

“He came down that escalator and immediately started demonizing immigrants,” said Mr. Dubnau, 59, a professor at Stony Brook University. “And so this is a symbolic spot where we’re here to say ‘no more.’ We won’t tolerate that.”

Building security officers turned up the music in the lobby and stopped more people from joining the group. After about 15 minutes, police officers who had been watching from afar warned that protesters who remained on the premises would be subject to arrest. Some began to slowly stream out; others stayed seated and continued to chant.

Roughly an hour after the protest started, more than two dozen officers began detaining demonstrators, zip-tying their hands behind their backs, lifting them to their feet and carrying them up the escalator.

Below, protesters continued chanting.

“We will not comply,” they said. “Mahmoud, we are by your side.”

White House officials have justified Mr. Khalil’s arrest by suggesting that by organizing protests on Columbia’s campus, he “led activities aligned to Hamas.” Officials have not accused Mr. Khalil of having any contact with Hamas, taking direction from it or providing material support to it.

His arrest marked an escalation of the Trump administration’s efforts to crack down on the protests, which officials have described as antisemitic and a threat to the safety of Jewish students.

The protesters at Trump Tower, many of whom were Jewish, pushed back on that notion.

One of them, Jane Hirschmann, 78, said that she believed Jews had a particular obligation to voice their opposition to the Trump administration because it had “weaponized antisemitism.”

Ms. Hirschmann, the descendant of Holocaust survivors, said Mr. Khalil’s arrest reminded her of family stories from that “terrible time,” when her grandfather and uncle were taken away in the middle of the night.

“I know, personally from my family history, I know what fascism is, I know what genocide is, I know what abduction is,” Ms. Hirschmann said.

Moments later, she was arrested.

James Schamus, a Columbia professor who participated in the protest and is Jewish, said he thought the notion that the campus was “somehow a hotbed of antisemitic intolerance” was ridiculous.

“We all know that if anything, Columbia is a hotbed of students raising their voice and conscience, and in protest against the inhumane policies that this regime is imposing,” he said.

Plans for the event came together in 36 hours, said Sonya Meyerson-Knox, a spokeswoman for Jewish Voice for Peace.

“As Jews, we know our history,” she said. “We know what happens when authoritarian regimes start scapegoating people and start taking away rights; we know exactly where that leads.”