In 1959, Lipon became a minor league manager, beginning at the Class D level with the Selma Cloverleafs of the Alabama–Florida League in the Cleveland Indians' organization. Lipon spent 30 of the next 34 years as a manager in the Cleveland, Detroit and Pittsburgh Pirates farm systems, winning 2,185 games and losing 1,987 (.524). He spent part of the 1961 season as manager of the Triple-A Toronto Maple Leafs of the International League, and his success as skipper of the Portland Beavers of the Pacific Coast League in the mid-1960s earned him a promotion to the Indians' coaching staff, where he served from 1968–1971.