On November 29, 2022, Auburn University announced that it had hired Freeze to be the 31st head coach of the Auburn Tigers football team.
Freeze was named head coach of the Liberty Flames football team on December 7, 2018. In his first year with the team, the Liberty Flames played to a 7–5 record, qualified for bowl games for the first time in school history, and accepted an invitation to the Cure Bowl in Orlando, Florida.
On December 5, 2011, Freeze was announced as the 37th head coach of the University of Mississippi. During the press conference to introduce him as the head coach, Freeze said he wanted to "retire at Ole Miss."
University of Mississippi
In 2010, he joined the staff of head coach Steve Roberts at Arkansas State as offensive coordinator. After the season, Roberts was fired and Freeze was promoted to head coach. In 2011, his only season as head coach at Arkansas State, he led the Red Wolves to a 10–2 record and their first Sun Belt Conference title since 2005.
Arkansas State University
In January 2008, Lambuth University, a member of the National Association of Intercollegiate Athletics (NAIA), named Freeze its head coach. In 2008, he led Lambuth to an 8–4 record and a first round loss in the NAIA playoffs. In 2009, he led the Eagles to their best regular season record in school history with an unblemished 11–0 mark.