Shelton was the minor league hitting coordinator for the
Cleveland Indians organization from 2003, until he replaced major league hitting coach
Eddie Murray on an interim basis in the midst of the 2005 season. Shelton became the
Tampa Bay Rays' hitting coach after the 2009 season. The Rays fired him in September 2016. On December 12, 2016, the
Toronto Blue Jays hired him as a quality control coach for the 2017 season. On November 6, 2017, the
Minnesota Twins hired Shelton as bench coach for the 2018 season. On November 27, 2019, Shelton was named the manager of the
Pittsburgh Pirates. Shelton became the 41st manager in club history. On April 22, 2023, the Pirates announced that Shelton's contract had been extended. On May 8, 2025, the Pirates fired Shelton after a 12–26 start to the 2025 season. On October 29, 2025, the
Minnesota Twins hired Shelton to be the team's new manager according to
ESPN. The club confirmed this the following day.
Managerial record ==Personal life==