After six years in Dallas, Weiss accepted his first head coaching job in 1986 with the San Antonio Spurs. He coached the Spurs for two seasons, never posting a winning record. He did, however, lead them to the playoffs in 1988.
After one year as an assistant with the Orlando Magic, Weiss moved to the Atlanta Hawks as head coach. In three seasons, his Hawks teams posted a record of 124-122 and made the playoffs twice.
Weiss left the Hawks in 1993. He spent one year as head coach of the Los Angeles Clippers before joining the SuperSonics as an assistant coach. He served in that post for 12 years under both George Karl and Nate McMillan, going to the NBA Finals in 1996. He was promoted to head coach in 2005 after McMillan left for the Portland Trail Blazers. However, Weiss did not last even one season, as the Sonics struggled to a losing record. After a 13-17 start to the 2005-06 season, his three-year deal was terminated on January 3, 2006 and he was replaced with Bob Hill.
Weiss is the only person to be affiliated with the Clippers' franchise in all three cities of the organization's history. He was a player with the Buffalo Braves, an assistant coach with the San Diego Clippers, and a head coach with the Los Angeles Clippers. Weiss's all-time regular season NBA coaching record is 210-282 (42.7%).