In 1987 he was promoted to commander of the Seventh Brigade, Villavicencio, where he developed the plan of dismantling the laboratories and eradication of illicit activities by the Revolutionary Armed Forces of Colombia ()(FARC). Three years later he was given the position of commander of the Fourth Brigade in Medellín, Antioquia, where he participated in anti-narcotic operations against drug kingpin Pablo Escobar. In 1991 Bedoya was given the position of director of the Superior Military School in Bogotá, Cundinamarca. The following year he was again promoted to deputy commander of the Northeastern Division, a position he held for three years before being finally promoted in 1996 to commander-in-chief of the armed forces, where he replaced Admiral Holdan Delgado; he held that position for one year.