Shines served as the first base coach for the New York Mets for the 2009 and 2010 seasons. In 2011, he was replaced by Mookie Wilson. In 2012, he was the hitting coach for the Great Lakes Loons, the A team of the Los Angeles Dodgers. In 2013, he became the manager of the Loons and in 2014 he was promoted to manager of the Chattanooga Lookouts in the Double-A Southern League. The Dodgers switched Double-A affiliates for 2015, and Shines became the manager of the Tulsa Drillers of the Texas League. Despite being chosen by "Baseball America" as the best managerial prospect in the Texas League, Shines' contract was not renewed by the Dodgers after the season.