He stayed with the Blue Jays system when he began his managerial career in 1985. He managed the Medicine Hat Blue Jays, the GCL Blue Jays, the St. Catharines Stompers, the Dunedin Blue Jays, and the Tennessee Smokies. After the 2002 season, Wheeler was let go by the Toronto front office, and he moved over to the Atlanta Braves farm system managing the Rome Braves (2003–05) and the Myrtle Beach Pelicans (2006-2010). 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.[1] 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.