 After retiring as a player, Banister remained with the Pirates'organization. From 1994 through 1998, Banister served as a manager in the Pirates' minor league system. He served as the manager of the Welland Pirates of the New York – Penn League in 1994. A year later, he managed the Augusta GreenJackets of the South Atlantic League, and led them to win the league's championship. Banister managed in the Hawaiian Winter League in the 1995 and 1996 offseasons. From 1996 through 1997, he was the manager of the Lynchburg Hillcats of the Class A-Advanced Carolina League. Midway through the 1997 season, he was named the manager of the Carolina Mudcats, a position he held through the 1998 season. Banister had a 299 – 330 win-loss record (a .475 winning percentage) as a manager from 1994 through 1998.
