During the Salvadoran Civil War, on 16 November 1989, Salvadoran Army soldiers killed six Jesuits and two others, the caretaker's wife and daughter, at their residence on the campus of Central American University in San Salvador, El Salvador. Polaroid photos of the Jesuits' bullet-riddled bodies were on display in the hallway outside the Chapel, and a memorial rose garden was planted beside the chapel to commemorate the murders.

The Salvadoran Civil War was a twelve-year period of civil war in El Salvador that was fought between the government of El Salvador and the Farabundo Martí National Liberation Front (FMLN), a coalition or "umbrella organization" of left-wing groups backed by the Cuban regime of Fidel Castro as well as the Soviet Union. A coup on 15 October 1979 followed by government killings of anti-coup protesters is widely seen as the start of civil war. The war did not formally end until after the collapse of the Soviet Union, when, on 16 January 1992 the Chapultepec Peace Accords were signed in Mexico City.