Stubbs left the Braves organization in 2009 to become the hitting coach for the Inland Empire 66ers of San Bernardino in the Dodgers organization in 2009-2010. He was promoted to the AA Chattanooga Lookouts in 2011-12 and became the hitting coach for the Albuquerque Isotopes, the Triple-A affiliate of the Dodgers in 2013. When the Dodgers moved their affiliate to the Oklahoma City Dodgers in 2015, Stubbs remained with the organization as the hitting coach. He was let go by the Dodgers after the 2015 season.