At the close of 1989, an end to the fighting seemed a remote dream. Yet in April 1990, representatives of both the FMLN and the government, under the chairmanship of the UN, met in Geneva for the first of a series of negotiations that would lead to peace. This was achieved largely due to global changes: the end of the Cold War had reduced Central America's strategic importance, and both the US and USSR switched policy to an active encouragement of conflict resolution. Increasingly isolated and drawn into a military stalemate, both the government and the FMLN bowed to US and UN pressure to seek a negotiated solution.

A protracted negotiating process resulted in a UN-brokered agreement, the Chapultepec Accords , signed on January 16, 1992, followed on February 1 by a formal ceasefire. The FMLN agreed to disengagement and demobilization of its forces; the government to a purge of the armed forces and reduction in its size. In addition, a number of civil institutions were to be created, including a new civilian police force (the PNC), a human-rights institution and a "Truth Commission". The UN set in place a resident observer mission (ONUSAL) to verify compliance within a set time limit. A land transfer programme, expected to transfer ten percent of agricultural land to demobilized combatants and refugees, was inaugurated and a tripartite commission, including the government, workers and private sector, set up to formulate further social and economic policies. On December 15, 1992, the day the FMLN registered as a formal political party, the civil war was formally ended.