After the restoration of democracy, he served in the Cabinet of President Corazon Aquino as Secretary of Environment and Natural Resources (Philippines) (DENR) from 1987 to 1992.
[2] 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.
[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.
[2] Factoran had served on the board of directors for Rappler, a major Filipino online news site from 2018 until his death in 2020.
[1] He was predeceased by his wife, Kaye Mesina, and survived by their four children, Yazmin, Gertrude Anne, Fulgencio III, and Roberto Carlo.