Despite the injury that could have jeopardized his football scholarship, Auburn continued his funding, and baseball became his sole sport. He won consideration for the U.S. National Team – preparing for the 1988 Summer Olympics – but was cut from the final squad. By the end of his junior baseball season he had hit 19 home runs, 19 doubles, and batted .403 with a slugging percentage of .801. He earned Southeastern Conference MVP honors his senior year. Thomas concluded his college career with 49 home runs, a school record. In May 2011, he was inducted into the Alabama Sports Hall of Fame.