As a full-time manager, Scheffing led the Los Angeles Angels of the Pacific Coast League to the 1956 PCL championship, and was promoted to skipper of the parent Cubs the following season. In three full years at the Cubs' helm, Scheffing compiled a 208–254 (.450) record. His 1957 team finished 62–92 and tied for seventh place in the eight-team National League, but his 1958 and 1959 clubs won 72 and 74 games respectively and finished tied for fifth place each season.