In 1989, Leyva was hired as manager of the Phillies by his former farm director in St. Louis, Lee Thomas. 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. In 1990, his team won ten more games and finished fourth, but still played eight games below the .500 mark. When the 1991 Phillies dropped nine of their first 13 games, Leyva was ousted on April 23. His career totals as a Major League manager were 148 victories and 189 defeats (.439).