In 1995, Miles left to accept his first head coaching job at NAIA II Mayville State.

In both his seasons at Mayville State, Miles led the Comets to NDCAC Championships and the NAIA II National Tournament.

Southwest State won the North Central Region Championship and advanced to the NCAA II Elite Eight in Bakersfield, CA.

The Bison, starting three freshmen, ended Wisconsin's 27-game home winning streak against non-conference opponents.

On March 22, 2007, Miles was named head coach at Colorado State, replacing Dale Layer.

In May 2011, after winning 19 games and guiding CSU to its seventh NIT appearance, he signed a 5-year contract extension with Colorado State.

On March 24, 2012 Miles was named head coach at Nebraska, replacing Doc Sadler.

Miles was relieved of his duties on March 26, 2019, finishing as the coach with the third-most wins in Nebraska men's basketball history.

Nebraska athletic director Bill Moos stated that “Ultimately, we have not maintained a level of consistent success and stability on the court, and after a full review I have made the decision to move in another direction for the leadership of our program.”[6] On April 6, 2021, Miles was hired as the head men's basketball coach at San Jose State University.

During his time away from coaching, Miles served as an analyst for the Big Ten Network, Fox Sports, and FS1.