Leyva served on the big-league coaching staff of Whitey Herzog's Cardinals for five seasons, 1984–1988. He was the first base coach for the National League-champion Cardinals in 1985, and the third base coach for the NL-champion Cardinals in 1987.
In 1989, Leyva was hired as manager of the Phillies by his former farm director in St. Louis, Lee Thomas (who himself was serving as the Phillies' general manager).[4] The Phillies won only 67 of 162 games during Leyva's inaugural season at the helm, and finished last in the National League East Division.[5] In 1990, his team won ten more games and finished fourth, but still played eight games below the .500 mark.[5] When the 1991 Phillies dropped nine of their first 13 games, Leyva was ousted on April 23.[6] His career totals as a Major League manager were 148 victories and 189 losses (.439).[5]
Coach with Blue Jays, Brewers and Pirates
After managing the Toronto Blue Jays' Triple-A farm team, the Syracuse Chiefs, Leyva spent 4+1⁄2 seasons (July 1993–1997) as the third-base coach of the Blue Jays, his first term in the job. As a major league manager and coach, Leyva has worn #16 with every team he has been with, except for his first year in Toronto in 1993, during which he wore #45 as #16 was already taken. He later worked at multiple levels of the Chicago White Sox farm system before spending one season as third-base coach of the Milwaukee Brewers in 2007.
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.[7] 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.[8] On November 8, 2010, former Seattle Mariners manager Don Wakamatsu was named Toronto's bench coach, ending Leyva's tenure at that post.[9]
On November 24, 2011, Leyva was named the Pittsburgh Pirates' third base coach, under new manager Clint Hurdle.[10] On November 5, 2014, the Pirates announced that Leyva would be moved to first base coach and Rick Sofield would move from first base to third base.[11] On October 22, 2016, the Pirates announced that Leyva was reassigned within the organization to an advisory position and would no longer coach.[12]
Coach in Venezuela
Leyva managed the Cardenales de Lara of the Venezuelan Professional Baseball League in 1995-1996 season, leading them to the finals where they lost against the Navegantes del Magallanes, four games to three. For the 2000-2001 season, he again managed the Cardenales, leading them to his fourth championship in Venezuela, defeating the team that defeated him four years before in six games. Seven years later, he returned to Venezuela to manage the Navegantes del Magallanes in the 2008-2009 season, but was dismissed because of the team's poor record.