When Mullins retired in 1996, Watkins was promoted and became the seventh head coach in school history and the first Charlotte alumnus to hold the position.
He compiled an overall 42–20 record in his two seasons as head coach, bringing the 49ers to the NCAA tournament twice, reaching the second round each year.
[4] In one of the team's more controversial games of Watkins's A&M career, A&M beat Texas Tech 88–86 by sinking a basket at the buzzer.
The game was declared over, although Texas Tech administrators continued to plead with officials to return to the court and review the play.
The lead official was later suspended, not for missing the call, but for failing to follow procedure for returning to the court after declaring the game was over.
[2] After tendering his resignation at Texas A&M, Watkins accepted the job as associate head coach at the University of Missouri on June 21, 2004.
[2] Watkins was named interim head coach at Mizzou following Quin Snyder's firing on February 10, 2006, with the Tigers at a record of 10–11 and suffering from a six-game losing streak.
Conference tournament champion *Interim coach after Quin Snyder resigned; complete record for the 2005–06 season was 12–16 (5–11 Big 12).