In 2002, he was appointed by President Gloria Macapagal Arroyo to be the executive director of the then-National Historical Institute. He was reappointed to the post by President Benigno Aquino III on December 2010. Historian Benito J. Legarda criticized Badoy's reappointment in a column published in the Philippine Daily Inquirer saying it was a "slap in the face of the government career service" and that Badoy "lacks the academic and career credentials for a historical agency". In 2015, there were calls for Badoy's resignation due in part to the Torre de Manila controversy. Badoy retired from the agency in 2020. During his term, he was credited with modernizing historical sites and museums under his office and for the successful commemorations of the birth sesquicentenaries of Jose Rizal, Andres Bonifacio, Apolinario Mabini, and Emilio Aguinaldo. His term also saw the restoration and reconstruction of heritage churches destroyed during the 2013 Bohol earthquake and Typhoon Haiyan which was partially funded by the NHCP.