For much of El Frontón's history, the island was used as a prison. Fernando Belaúnde Terry, who was twice president of Peru, was imprisoned on the island for twelve days as a political prisoner. During his imprisonment, Belaúnde Terry made an unsuccessful attempt to swim to freedom. Hugo Blanco was also imprisoned on the island.
During the insurgency of the Shining Path, the island was used as a prison for Maoist militants. On June 18, 1986, the Shining Path led an uprising on El Frontón as well as two other prisons. The government of Alan García treated the prisons as war zones, and the Peruvian Navy was sent to the island. Many of the prisoners involved in the rebellion were killed, and Human Rights Watch claimed that evidence suggested that "no fewer than ninety" of the prisoners killed were victims of extrajudicial executions.