Stein continued to manage the Columbia Mets in 1990, leading them to an 83–60 record. The Mets had the best record in the South Atlantic League that season. In 1991, Stein was hired to be the manager of the Bend Bucks of the Northwest League. The non-affiliated Bucks had a record of 30–46 with Stein as the manager. He was hired to be the manager of the Clinton Giants in 1992. Clinton was the Class-A affiliate of the San Francisco Giants at the time. Stein led Clinton to a 59–79 record that year. After considering taking a year off of baseball in 1994, Stein eventually accepted the managerial position with the independent league Tyler WildCatters.