Since his playing career, Cantú has been active in Mexican soccer administration. He was the director of national selections for the Federación Mexicana de Fútbol Asociación from 2004 to 2009, when he resigned after Mexico failed to qualify for the 2009 FIFA U-20 World Cup. He also served as president of Santos Laguna and Chiapas, holding the latter post from 2010 to 2012.