He remained with the Storm through the 2013 season and then was hired as hitting coach for the Double-A Chattanooga Lookouts in the Dodgers organization. In 2015 the Dodgers switched their Double-A affiliation to the Tulsa Drillers and he remained the hitting coach for them. He was promoted to hitting coach for the AAA Oklahoma City Dodgers of the Pacific Coast League in 2016. He left his position with the Dodgers after the 2017 season. Wooten was employed by the Los Angeles Angels as a minor league hitting director in 2017. In the offseason, Wooten operates a baseball academy for young kids to high schoolers (and sometimes working with college players) in Plymouth, Minnesota. Following his minor league job, Wooten was promoted to the position of Assistant Major League Hitting Coach for the Los Angeles Angels prior to the 2019 season. Wooten is a member of the Cedar Rapids Professional Baseball Hall of Fame.