Bonner is perhaps best known as one of two journalists (the other was Alma Guillermoprieto of The Washington Post) who broke the story of the El Mozote massacre, in which some 900 villagers at El Mozote, El Salvador, were slaughtered by the Salvadoran army in December, 1991. A Times staff reporter at the time, Bonner was smuggled by FMLN rebels to visit the site approximately a month after the massacre took place. When the story broke simultaneously in the Post and Times on January 27, 1982, it was dismissed as propaganda by the Reagan administration, as it seriously undermined efforts by the US government to bolster the human rights image of the Salvadoran government, which the US was supporting with large amounts of military aid. The Times was strongly criticized by the US government for running the story, and the newspaper was pressured to pull Bonner moved from the Central American desk. He left the Times shortly thereafter but still contributes to the paper as a freelance correspondent.
In 1992, the details of the massacre as first reported by Bonner and Guillermoprieto were verified, with widespread repercussions.