Following Bengie's departure from the Angels, Molina entered the 2006 season as the Angels' new starting catcher, though it was expected that rookie Jeff Mathis would also see substantial time handling the team's catching duties over the course of the season. However, Mathis struggled during the first month of the season and, as a result, he was ultimately demoted to the minor leagues. Molina himself then struggled offensively, and the promising offensive performance of Mathis' replacement on the roster, rookie Mike Napoli, once again relegated Molina to the role of backup catcher. Still, he played in a career-high 78 games and had a career-best 225 at-bats in 2006.