García Oliver eventually became the leader of the FAI. When the CNT reluctantly decided to enter the Popular Front government during the Spanish Civil War of 1936-1939, García Oliver served as Minister of Justice under Francisco Largo Caballero (1936-1937). He encouraged workers to disarm during the Barcelona May Days of May 1937, calling a ceasefire. Some consider him a traitor to the Spanish anarchists for his willingness to compromise with government, while others see his concessions as understandable considering the need to defeat Francisco Franco.
He left the government later in the same month, but remained active in Barcelona until Catalonia fell in 1939, taking refuge in France, then Sweden, and finally in Mexico (where he remained until his death).