Mendoza became a member of the Bench in 1989 when he was appointed presiding judge of the Regional Trial Court of Sta. Cruz, Laguna. He eventually became the executive judge of the same court in 1992. In 1994, he was designated presiding judge, and later on as executive judge, of the Quezon City Regional Trial Court. After 15 years as a judge, he was appointed Associate Justice of the Court of Appeals on July 4, 2003. One of his well-known decisions as an appellate justice was the reinstatement of the criminal charges against millionaire businessman Dante Tan, an ally of former President Joseph Estrada who was involved in a stock price manipulation scandal. He also penned the decision approving the petitions for the writ of amparo and the writ of habeas corpus filed by the families of University of the Philippines students Sherlyn Cadapan and Karen Empeño, who were allegedly abducted by the members of the military in 2006. On January 4, 2010, he was appointed Associate Justice of the Supreme Court to replace erstwhile Associate Justice Minita Chico-Nazario. His first major decision as a member of the Supreme Court was the controversial , where he struck down as unconstitutional President Benigno Aquino III's Executive Order No. 1 creating a Truth Commission to investigate corruption during the administration of former President Gloria Macapagal-Arroyo. Together with nine of the 15-member tribunal, he invalidated the executive order because of its apparent transgression of the equal protection clause for singling out the Arroyo administration. In his ponencia, Mendoza blatantly tagged Aquino's Truth Commission "as a vehicle for vindictiveness and selective retribution." Justice Mendoza also wrote the high tribunal's decision in striking down as unconstitutional eight major provisions of the highly divisive Reproductive Health Law, which was strongly opposed by religious conservatives in the country. Mendoza nonetheless upheld the validity of the remaining provisions of the RH Law despite his strong affiliation with the influential Catholic Church. In his ponencia, the magistrate highlighted the constitutional principle of separation of church and state, stressing that "the church cannot impose its beliefs and convictions on the State and the rest of the citizenry. It cannot demand that the nation follow its beliefs, even if it sincerely believes that they are good for the country."
