Perhaps in an effort to make amends for the means by which he came to office, Lemus initially took some conciliatory steps, such as declaring a general amnesty for political prisoners and exiles, voiding a number of repressive laws left over from previous regimes, and selecting men of recognized probity and ability for his cabinet. The course of his administration, however, was dominated by economic events. A decline in the export prices of coffee and cotton and the resultant drop in income and revenue exposed the weakness of the PRUD's limited reforms. Heavy-handed political manipulations by the government and the party, in particular the approval of a new electoral law that all but precluded an effective opposition, exacerbated widespread dissatisfaction with the Lemus government. After 1959 the influence of what then appeared to be a popular, nationalistic revolutionary movement in Cuba was felt in El Salvador as it was throughout Latin America. Student groups were particularly inspired by the example of Fidel Castro Ruz and his revolutionaries. Public demonstrations in San Salvador called for Lemus's removal and the imposition of a truly democratic system. The president responded by abandoning his earlier efforts at reform in favor of heightened repression. Free expression and assembly were banned, and political dissidents were detained arbitrarily.

This instability provoked concern among important political actors in El Salvador. For the elite, the government's emphasis on economic development was pointless under such a climate; the emerging middle class likewise felt a threat to its gains from the specter of revolution; and the military reacted almost reflexively to the spectacle of a president who had lost control. Lemus was deposed in a bloodless coup on October 26, 1960.

Governmental authority again passed into the hands of a military-civilian junta. The ranking military representative was Lieutenant Colonel Julio Adalberto Rivera. Aside from Rivera, the junta member who drew the most attention was Fabio Castillo, a university professor and known sympathizer with the Cuban Revolution.