Purdue After one year as an assistant coach at
West Lafayette High School, Martin returned to Purdue in 2000 to be an assistant coach under his former coach
Gene Keady and former teammate,
Matt Painter. He helped the Boilers to an
Elite Eight appearance and three
NCAA Second Round appearances, along with an overall 153–129 record during his eight seasons on the Purdue bench. He was named associate head coach for the 2007–08 season.
Missouri State After eight seasons at Purdue, Martin accepted the head coaching position at Missouri State University on March 25, 2008. He replaced
Barry Hinson. After falling to
Auburn in the season opener, Martin had his first head coaching win over
Central Michigan on the road. Martin's Bears won their first game at their new
JQH Arena home, beating
Arkansas from the
SEC. They wrapped up the pre-conference season with a 7–4 record. Martin's Bears headed into conference play with only 3 players appearing in every game, due to a number of injuries. They lost their first conference game in overtime against an undefeated
Illinois State. His Bears finished the season with an 11–20 record. Following his first season as head coach, Martin's top 25
RPI-ranked Bears started the 2009–10 season with a 10–0 start. Missouri State averaged a 10+ margin in points per game coming into Missouri Valley Conference play. Cuonzo's squad finished seventh in conference play with a 20–12 record and accepted a bid to the
CIT tournament, which they ended up winning to finish the season with a record of 24–12. In Coach Martin's third year at Missouri State, the team won their first regular season Missouri Valley Men's Basketball title and entered the
Arch Madness conference tournament as the #1 seed. After reaching the finals, they lost to the Indiana State Sycamores. Although having an RPI of 44, the team was not selected as an at-large team to the 2011 NCAA Men's Basketball tournament. They accepted a bid to the
National Invitation Tournament, beating Murray State University at home and then losing to Miami (FL) away in the 2nd round. The team ended the season with a 26–9 record.
Tennessee On March 27, 2011, after three seasons at Missouri State, Martin was hired as the head coach of the
Tennessee Volunteers. In three seasons as head coach, Martin led the Volunteers to two
NITs and to the
2014 NCAA tournament Sweet Sixteen. After a slow start to the 2013–14 season, several fans began openly campaigning to have Martin replaced with his predecessor,
Bruce Pearl, who was about to finish serving a
show-cause penalty. An online petition urging athletic director
Dave Hart Jr. to rehire Pearl drew 40,000 signatures. Later, Martin said that several of his own players were displeased with the way fans treated him.
California On April 15, 2014, Martin was hired as the head coach of the
University of California, Berkeley men's basketball team. In 2015–16, his second season, the Bears were led by freshman All-Americans
Jaylen Brown and
Ivan Rabb to a 23-win regular season and a number 4 seed in the South Region of the
NCAA tournament, where they lost in the first round. Cal began the season ranked in the top 25 but fell out and resurfaced ranked 25th in early March after losing only one game in February, to #18 Arizona by 3 points. On October 25, 2016, Martin agreed to a contract extension through the 2020–21 season. Following Cal's loss in the first round of the
2017 National Invitation Tournament, Martin announced his resignation as head coach on March 15, 2017. Martin left for Missouri, with Cal facing the "likelihood of a depleted roster (the) next season".
Missouri On March 15, 2017, the same day as his Cal resignation, Martin was hired as the head coach of the
University of Missouri men's basketball team. On March 24, 2017, Martin received the commitment of top recruit and Missouri native
Michael Porter Jr., also adding his father, Michael Porter Sr., to his coaching staff. He was
released from his position on March 11, 2022, after finishing 78–77 overall and reaching two NCAA Tournaments. On March 27, 2024, it was publicly announced that Martin would return to Missouri State as the men's basketball head coach ==Coaching notes==