On November 15, 2012, Governor-elect Alejandro García Padilla appointed Bernier to succeed Kenneth McClintock as Puerto Rico's 23rd Secretary of State, which also entails the role of lieutenant governor. At the moment, Bernier was preparing to be reelected as President of the Olympic Committee when he was approached by García Padilla for the position. He was sworn into his recess appointment by Puerto Rico Supreme Court Chief Justice Federico Hernández Denton and he has since been unanimously confirmed by the Senate of Puerto Rico and the Puerto Rico House of Representatives. Holding the title of Secretary of State entails serving in the dual role of lieutenant governor. As such, he has served as acting governor whenever Governor García Padilla has been out of Puerto Rico. At least once during his term, the acting governorship has been delegated to Attorney General Luis Sánchez Betances when both the Governor and Bernier have been absent, and when General Sánchez Betances has also been away, Secretary of the Treasury Melba Acosta has served as acting governor.