In 2009, he wore the captain armband as he and his team won the Apertura 2009 tournament by beating Cruz Azul at Estadio Azul in Mexico City. In the championship season, Pérez appeared in 18 matches, scored three goals and registered two assists. He also won the 2010 InterLiga with Monterrey, beating América in penalty kicks, that qualified Monterrey into the 2010 Copa Libertadores. On June he became property of Guadalajara, by an agreement between the manager of C.F. Monterrey and the sporting director of Chivas, Michel Leaño. On 7 July he scored his first goal with Guadalajara.