Mizerock's first managerial job came with the rookie league Eugene Emeralds in . After leading the team to a 40-36 record, he was promoted to the Class A Rockford Royals in , where he earned Midwest League Manager of the Year honors. He moved to the Carolina League's Wilmington Blue Rocks in , where he was again named his league's manager of the year. In 1996, Wilmington won the league championship with Mizerock at the helm. He remained with Wilmington through before moving on to the Wichita Wranglers in . He won the Texas League title and was Minor League Manager of the Year with Wichita in . He spent the & seasons with the Omaha Golden Spikes before getting his first major league coaching gig with the major league club in . He compiled 646 wins and 554 losses in his minor league managerial career.