After retiring, Bowa was named manager of the Las Vegas Stars, the Triple-A affiliate of the San Diego Padres, for the 1986 season. In Bowa's only season at the helm, the Stars went 80-62 en route to the Pacific Coast League championship. Bowa was hired to manage the Padres on October 28, 1986, a little over a year after playing in his final MLB game. His aggressive and often angry style combined with an extremely young and inexperienced roster led to a down 1987 season in San Diego, and when higher expectations for the 1988 team (mainly engendered by those young players showing greatly improved performances in the 2nd half of the 1987 season and the 1988 spring training slate) were not met, he was fired on May 28, 1988 with an overall record of 81-127 as the club's skipper.