Leiper's coaching career began while he was still an active player:he spent part of the 1992 season as an assistant baseball coach for North Carolina State University. In 1996,Leiper became a coach in the professional ranks,in the New York Mets' organization.[4] He moved up to managing in 2000 in the Montreal Expos' organization,working at the Short Season-A and Class A levels before his promotion to the Triple-AOttawa Lynx of the International League in 2002. After Leiper guided the Lynx to 80 wins in 143 games that season,he spent one season as manager of the Class A Sarasota Red Sox before returning to the Lynx in 2004,who were by then the Triple-A affiliate of the Baltimore Orioles. Leiper then spent four seasons in the Pittsburgh Pirates' system,including three as manager of the Double-AAltoona Curve,before joining the Florida Marlins in 2009.[5] In 2010,he managed the Jacksonville Suns,the Marlins' Double-A affiliate,[6] where he led them to the 2010 Southern League championship. He then served as the Marlins' roving minor league defensive coordinator in 2011 and 2012. In 2013,he was senior advisor for minor league operations for the Toronto Blue Jays before his promotion to Blue Jays manager John Gibbons' staff for 2014,his first year in Major League Baseball after 29 years as a minor league player,manager and instructor.
After manager John Gibbons parted ways with the Toronto Blue Jays after the 2018 season,Leiper was fired on November 3,having served as Toronto's first base coach since 2014.[8]
Leiper was hired by the San Diego Padres as the third base coach for the 2024 season.[9]
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