In the aftermath of the 1986 People Power Revolution which ousted Marcos, Factoran was appointed as deputy executive secretary to President Corazon Aquino from March 1986 to 1987.[2][3]
He then served as Secretary of Environment and Natural Resources (Philippines) (DENR) in President Aquino's Cabinet from 1987 until 1992.[2] During his tenure as DENR Secretary, Factoran revoked many of the logging concessions that had been awarded during Marcos' rule.[3] He created new programs to promote reforestation efforts and reverse the extensive deforestation in the Philippines.[3] He also transferred stewardship of forests to local residents and communities.[3] Factoran opened the DENR archives to journalists, including Marites Vitug for her 1993 book "Power from the Forest: The Politics of Logging" to expose the abuses of the country's natural resources during the Marcos regime.[3]
Jun Factoran died from a longtime illness on April 5, 2020, at the age of 76.[1] He was predeceased by his wife, Kaye Mesina, and survived by their four children, Yazmin, Gertrude Anne, Fulgencio III, and Roberto Carlo.[1]