A successful coach in NAIA (Mayville State) and NCAA Division II (Southwest Minnesota State), Miles took over at North Dakota State in 2001. Shortly thereafter, the school declared its intent to reclassify from Division II and transition to Division I. The school would be ineligible for postseason play in its first five years of the transition, and was initially without a conference. On January 21, 2006, in just the school's second year in Division 1, NDSU pulled off a shocking 62–55 upset of #12 Wisconsin at the Kohl Center. The Bison, starting three redshirt freshman, ended Wisconsin's 27-game home winning streak against non-conference opponents. Miles would be named the Division I Independent Coach of the Year by CBS Sportsline.
The following season the Bison pulled yet another stunning upset. NDSU won at #8 Marquette in the championship game of the school's Blue and Gold Classic 64–60. The Bison would go on to finish 20–8, their best season under Miles. Of note, one year after Miles departed, at which time the school had since gained entry to the Summit League, the Bison made the NCAA Tournament under Miles' top assistant and successor, Saul Phillips, in their first year of eligibility primarily with the same players (as seniors) Miles had recruited and coached during their upsets of Wisconsin and Marquette.
On March 22, 2007, Miles was named head coach at Colorado State, replacing Dale Layer. Miles inherited just two players from the 2007 roster, and struggled to succeed early, going so far as to hold walkon tryouts to fill his first roster. After going winless in conference during his first season, Miles' teams improved gradually in the following years.
In May 2011, after winning 19 games and guiding CSU to its seventh appearance in the NIT during the 2010-11 season, he signed a 5-year contract with Colorado State.
The 2011-12 season saw Miles once again pulling upsets over ranked opponents. On January 28, CSU upset #12 San Diego State 77-60 at Moby Arena, marking the program's first win over a ranked opponent since 2004. Just over a month later the Rams stunned #18 New Mexico 71-63. Then, on February 29, Colorado State rallied from down 15 at half to defeat #17 UNLV 66-59. All three wins came at Moby Arena where CSU went 14-1, including 7-0 against Mountain West teams, the program's first perfect home season in conference play since 1960. Finishing with a 20-11 overall record, 8-6 in the Mountain West, Colorado State was awarded an at-large bid to the NCAA Tournament. It was CSU's first trip to the NCAA Tournament since 2003 and their first at-large bid to the field since 1990. The Rams were the 11th seed in the West Regional and fell to 6th seed Murray State.
On March 24, 2012 Miles was named the next head men's basketball coach at the University of Nebraska, replacing Doc Sadler. In the 2013-14 season, he coached Nebraska into the NCAA Tournament, the first time Nebraska had made the tournament since 1998.
National champion Postseason invitational champion Conference regular season champion Conference regular season and conference tournament champion Division regular season champion Division regular season and conference tournament champion Conference tournament champion