Shipley began switch-hitting in college at the suggestion of his coaches.[3] Before the start of the 1986 season, after struggling offensively for two seasons in the minors, he reverted to batting exclusively from the right side of the plate.[5]
Shipley's post-playing career began in 2000, when he was a roving minor league baserunning and infield instructor for the Montréal Expos. He then returned to the Padres as a professional scout, working for Towers, in 2001–2002.
In 2003, Shipley followed former Padres executives Larry Lucchino and Theo Epstein to the Boston Red Sox, where he began as special assistant to the general manager, player development and international scouting. He was named a vice president in 2006, and was appointed senior vice president, international scouting, in 2009. In February 2011, Shipley was promoted again, when he was named senior vice president, player personnel and international scouting.[6] However, weeks after Epstein departed the Red Sox for the Chicago Cubs in October 2011, Shipley was dismissed in an overhaul of the Boston front office under the team's new general manager, Ben Cherington.[7]
In 2012, Shipley was hired by the Arizona Diamondbacks as an assistant to general manager Kevin Towers.[8][9] As of 2022[update], he is still part of the Diamondbacks front office, assisting "the Baseball Operations Department in international and special assignment scouting, evaluating the D-backs' farm system and serving as an advisor to the GM."[10]