Wheeler was named the manager of the Mississippi Braves on November 18, 2010. On June 22, 2017 he was named the manager of the Florida Fire Frogs of the Florida State League. Wheeler returned to the Braves organization as manager of the Rome Braves for the 2018 season, he will manage the Auburn Doubledays for the 2019 season.
Wheeler was appointed as the manager of the Mississippi Braves on November 18, 2010. On June 22, 2017 he took over as the manager for the Florida Fire Frogs in the Florida State League. For the 2018 season, Wheeler returned to manage the Rome Braves, and will manage the Auburn Doubledays in 2019.