Authorities said 194 people were taken to a gym to have their asylum applications processed, while an additional 160 "illegal occupants" were removed from the Paris-8 university in Seine-Saint-Denis, just north of the capital.
About 70 students and activists, alerted to the imminent operation, had slept on site and formed a human chain to try to keep out the police, who used tear gas to get inside.
The migrants, mainly from West Africa or Sudan and Eritrea, had been sleeping on the streets of Paris when pro-refugee activists invited them to occupy the university site in January.
Issa, who arrived at the site from Libya a month ago, told the AFP news agency he did not know exactly where he was going, but said he hoped to be allowed "to make his life" in France.
He and others had been having French classes while taking turns with cooking and cleaning duties and participating in a weekly general assembly -- translated into five languages.
In the spring they were joined by dozens of students protesting the government's plan to toughen admission requirements, part of months of university blockades across France.
Paris-8 chief Annick Allaigre said she asked security forces to intervene in order to repair an estimated 800,000 euros of damages on campus, and in response to cases of "violence" and theft.
About three dozen camps of closely packed tents have been cleared in the city over the past three years, underneath highway overpasses or elevated metro lines, or along the city's canals.
Some of the migrants have arrived in Paris from the northern port of Calais, where people have flocked for years hoping to stow away on trucks to Britain but where officials have vowed to prevent any new camp like the "Jungle", which was cleared in 2016.
Many are hoping for refugee status, but they may face expulsion under President Emmanuel Macron's tougher immigration laws, which speed up procedures to deport so-called "economic" migrants not considered at risk of persecution at home.