After retiring as a player, Mackanin spent many years managing and coaching in the minor leagues. He became the Expos' third base coach in 1997 and spent four years in that position. After managing the minor league Hickory Crawdads and Lynchburg Hillcats in 2001 and 2002, Mackanin became the bench coach for the Pittsburgh Pirates for the 2003 season. After Lloyd McClendon was fired, Mackanin served as the Pirates' interim manager for the last month of 2005, leading the team to a 12–14 record. He spent the next season managing in the Pirates' minor league system at Bradenton.