Since 2005, he has worked in the Mets organization, first as a roving hitting instructor, then as minor league hitting coordinator. With Johnson overseeing the development of young hitters, the Mets farm system has produced enough talent that on April 26, 2011, the team fielded a starting lineup of all homegrown players for the first time since 1971. On May 26, 2014, Johnson was made the new hitting coach for the Mets, replacing Dave Hudgens. He served through the end of the season, then was reassigned as a minor league hitting instructor in the Mets' organization. He was replaced by former Yankees' coach Kevin Long for the 2015 season.