After that disastrous season, Loughery retired as a player and became head coach of the American Basketball Association's New York Nets the following season. With superstar Julius Erving, Loughery won two ABA championships in three seasons. After the ABA disbanded and the Nets joined the NBA, Loughery continued to coach the Nets for their first five seasons in the league. The team would struggle in their first couple of seasons without Erving, whose contract was sold to the Philadelphia 76ers due to financial struggles. The team would also move to New Jersey and become the New Jersey Nets. He was fired midway through the 1980–81 season and replaced by Bob MacKinnon.
Loughery was hired by the Atlanta Hawks the very next season and he guided them to two straight playoff appearances, including one with rookie Dominique Wilkins. He was fired once again after the 1982–83 season and replaced by Mike Fratello.
The next two seasons, Loughery coached the Chicago Bulls. In his second season with rookie Michael Jordan, the Bulls made the playoffs. In the book The Jordan Rules Michael was quoted as saying that Loughery was the most fun coach he ever played for and that Loughery allowed him to free-lance and play the style he wanted.
Loughery went to the Washington Bullets the next season as an assistant to Gene Shue. When Shue was fired with 13 games left in the 1985–86 season, Loughery guided the team to the playoffs and once again the next season. The Bullets got off to a bad start in 1987–88 and Loughery was fired once again.
After working in broadcasting, Loughery was hired by the Miami Heat as their second coach three years after they joined the league as an expansion team. Loughery guided the Heat to their first ever playoff appearance and again in 1993–94.