After retiring from the NBA, Winters became an assistant coach for two years under legendary coach Pete Carril at Princeton. From there, he moved on to become an assistant coach under Hall of Famer Lenny Wilkens with the Cleveland Cavaliers for 7 years and Atlanta Hawks for two more. Next, he was the inaugural coach for the Vancouver Grizzlies for a year and a half. Later, Winters coached with the Denver Nuggets and Golden State Warriors. He was formerly the head coach of the WNBA'sIndiana Fever, leading them to their first ever consecutive-year playoff appearances.
On October 26, 2007, Winters option wasn't picked up by the Indiana Fever, ending his four-year tenure with the club. He compiled a 78–58 record in the regular season to go with a 5–7 playoff record. He was a scout for the Indiana Pacers for several seasons until he was let go during the NBA lockout in August 2011. He spent the 2012–13 season as an assistant coach with the Charlotte Bobcats.