In July 2005, Carter replaced Billy Joe to become the new head coach at Florida A&M University. In the 2005 and 2006 seasons, Carter compiled 6–5 and 7–4 records, respectively. After compiling a 3–8 record in the 2007 season, Florida A&M fired Carter, citing that the university needed to "move in a new direction".
On February 28, 2013, Carter was hired as the defensive line coach for the Purdue Boilermakers football team. On November 29, 2015, Carter's contract was not renewed by Purdue.