 After returning to Rochester in 1999 and serving as the Amerks captain in his final season, Houda retired after the 2002–03 season and immediately became an assistant coach under Randy Cunneyworth in Rochester.On July 25, 2006, Houda was named an assistant coach for the Boston Bruins.He was relieved of his duties following the 2015–16 season, after 10 seasons with the Bruins.