From 1980 until 1992, El Salvador was ripped apart by a civil war that left more than 75,000 people dead. During this time, the United States, fearing that El Salvador would succumb to a leftist takeover, poured funds into Salvadoran military operations. Although Moakley had been urging the Reagan administration to cut El Salvador’s military funding since the early 1980s, his commitment to El Salvador was cemented after meetings with constituents that included refugees of the Salvadoran civil war and a group of community activists, the Jamaica Plain Committee on Central America.
As a result of these encounters Moakley spent the next six years working to ease immigration restrictions on Salvadorans, and was later chosen to lead a congressional investigation into the 1989 murders of six Jesuit priests and two women at the University of Central America in San Salvador. This congressional investigation, also known as the Moakley Commission, revealed that the murders had been directed from the upper levels of the Salvadoran armed forces. The findings also resulted in reduced military funding to El Salvador, led to the successful prosecution of members of the Salvadoran military and helped pave the way for U.N. Peace Accords in 1992 and democratic elections in El Salvador. After the civil war ended, Moakley focused on closing the School of the Americas (SOA) and providing relief aid to the country after a series of natural disasters in the late 1990s.