Leyva was listed as the 2008 manager of the Kingsport Mets of the Appalachian League, a rookie-level affiliate of the New York Mets, before the Blue Jays rehired him as their third base coach on June 20, 2008, when Cito Gaston replaced John Gibbons as the club's manager. On October 30, 2009, Leyva was reassigned as the Blue Jays' bench coach, with Brian Butterfield taking over as third base coach for the team. On November 8, 2010, former Seattle Mariners manager Don Wakamatsu was named Toronto's bench coach, ending Leyva's tenure at that post.