Prosecutors on Thursday filed felony charges against 12 pro-Palestinian protesters — all but one of them a current or former student at Stanford University — for breaking into administration offices in June and causing extensive damage.

The charges were among the most severe levied against participants in last year’s pro-Palestinian demonstrations on college campuses. More than 3,000 people were arrested at college protests and encampments in the spring of 2024, but they generally faced misdemeanor charges or saw their charges dropped.

Jeff Rosen, the district attorney for Santa Clara County, which includes the Stanford campus, charged the 12 protesters with felony vandalism and felony conspiracy to trespass. They face up to three years and eight months in prison, as well as the payment of restitution to reimburse the university for the damage.

Stanford is one of dozens of schools being investigated by the Trump administration for how they have handled pro-Palestinian protests and whether they have done enough to combat antisemitism on campus. The administration has also revoked the visas of several Stanford students and recent graduates, though the reason is unclear. .

Mr. Rosen said that President Trump’s intense focus on Stanford and other universities played no role in the decision to charge the crimes as felonies.

“What the federal administration is doing is what they’re doing. What I’m doing is applying the California Penal Code,” Mr. Rosen said.

Mr. Rosen said he was swayed by the extent of the damage caused by protesters and what he characterized as deep, coordinated planning before the building was taken over.

“Whenever you have multiple people working together to commit a crime, it’s much more dangerous to the public,” he said. That the actions were intended to highlight the group’s opposition to the war in Gaza made no difference, he added.

“Speech is protected by the First Amendment,” he said. “Vandalism is prosecuted under the Penal Code.”

On June 5, police arrested 13 people in connection with breaking into the office of the Stanford president early that morning and barricading themselves inside. They made several demands, including that the university trustees vote on whether to divest from companies that support Israel’s military.

They were cleared out of the building and arrested within a few hours, but not before they had broken windows and furniture, disabled security cameras and splashed fake blood inside the building, Mr. Rosen said.

Mr. Rosen did not file charges against one of the 13 individuals, a student reporter for The Stanford Daily newspaper who was covering the protest, but not participating in it. Journalists and press freedom groups had demanded for months that Mr. Rosen decline to pursue charges against the student, Dilan Gohill, who was held in jail for 15 hours after his arrest, according to his lawyers.

Mr. Rosen said that his office undertook a deliberate, methodical investigation before determining that 12 of those arrested should be charged but that Mr. Gohill should not be. He announced in March there would be no charges for Mr. Gohill.

Mr. Rosen said the 12 protesters attempted to hide their communication, including the deletion from their phones of the Signal messaging app, through which they had exchanged messages shortly before their arrests.

He said his investigators were able to “work around” the protesters’ attempts to conceal their planning and found they had surveilled the building; studied the patterns of local police officers and security guards; and assigned themselves specific tasks, such as who would break the window and who would use a crowbar to pry open the door.

The protesters carried backpacks that were recovered in the barricaded building and contained hammers, chisels, screwdrivers and goggles, according to the Santa Clara District Attorney’s Office.

Tony Brass, a lawyer for one of the protesters, Hunter Taylor-Black, said that he was upset that Mr. Rosen took more than 10 months to file his charges. Ms. Taylor-Black, a 25-year-old Stanford film student, and other protesters had already completed their suspensions from the university and were beginning to put their lives back together, Mr. Brass said.

“The voice of student protest is an important voice in American history — always has been,” Mr. Brass said. “Everyone accepts there will be consequences for actions, and so did the protesters. But there was no need for adding this delay. Let them move on with their lives.”

The other 11 protesters either could not be reached or did not respond to requests for comment.

On the same morning as the protest, red graffiti appeared on the sandstone walls of the university’s main quad that condemned the police, Stanford, Israel and the United States. Phrases included “Pigs Taste Best Dead” and “Death to Israehell.” Mr. Rosen said he declined to file hate crime charges because his office could not prove that the 12 protesters were responsible for those messages.

Dee Mostofi, a spokeswoman for Stanford, said on Thursday that the university respected Mr. Rosen’s charging decisions. The university had separately levied its own sanctions on the protesters who were current students, including suspensions that lasted two quarters, a delay in degree conferrals and community service hours.

Mr. Rosen said he did not want to see the 12 Stanford protesters serve prison time. Instead, he said, he would like them to plead guilty and to join the Santa Clara County Sheriff’s work program, in which they would clean highways or government buildings.

“This is kind of biblical,” he said. “You trashed a building, so your punishment should be cleaning things up.”

Felony charges for pro-Palestinian protests on campus have occurred in at least several instances elsewhere over the past year.

Michigan’s attorney general brought felony charges against seven protesters at the University of Michigan, accusing them of resisting police officers who were breaking up an encampment in May 2024. Those cases are still pending.

At Case Western Reserve University in Cleveland, 11 people were charged with felony vandalism in February, a few months after they were accused of smearing red paint over buildings and a statue, causing $400,000 in damage.

At the University of Rochester in New York, four students were charged with felony criminal mischief after putting up “Wanted” posters with photos of university community members, including some Jewish officials, in November. The university’s president condemned the posters as antisemitic.

The severity of the charges stemmed from the cost of the damage caused by the posters, which were stuck to chalkboards and walls with “Super Glue or a similarly strong and durable adhesive,” according to court documents.

The charges are still pending.

Safa Robinson, a lawyer in Rochester who represents one of the students, said it was not unusual to see criminal mischief charged as a felony, since by law the seriousness is dictated by the cost of damage done. What is unusual, she said, is to see such a charge brought against student protesters.

“In a college environment, a lot of times posters are plastered all over the wall — frats, sororities, bake sales, elections, all that kind of stuff,” Ms. Robinson said in an interview. “I think that because these posters touched on a sensitive topic or had a certain type of view, that they’re being treated in this kind of way.”