After ending his playing days, he earned a position as an assistant coach at Purdue. He earned the top assistant position after two seasons, and then served one year at Illinois State. He then served two seasons at Miami (FL), where he helped guide the team to the 2001 College World Series title, produced two All-Americans, and saw 18 players sign professional contracts. He then moved to Tulane as recruiting coordinator, where six of his seven classes were ranked in the Top 25 nationally by Collegiate Baseball. The Green Wave reached the 2005 College World Series as the top seed, and earned academic honors in Omaha. In 2009, Kingston served as associate head coach at Illinois State before being elevated to the top job the following season.
Kingston was named the head coach at South Florida ahead of the 2015 season.
National champion Postseason invitational champion Conference regular season champion Conference regular season and conference tournament champion Division regular season champion Division regular season and conference tournament champion Conference tournament champion