After his retirement as a player, Magadan was hired by the Padres as their minor league hitting instructor in 2002, and served as their major league batting coach from 2003 to 2006. On June 15, 2006, with the Padres batting .252 as a team (last in the National League), Magadan was fired by Padres GM Kevin Towers and replaced by former Padres hitting coach Merv Rettenmund. Their .322 in on-base percentage and .391 slugging percentage was second to last to the Chicago Cubs.