Magni returned to management in 1958 with Serie C side Pro Patria and the club won promotion to Serie B in the 1959–60 season under his stewardship. Having guided them to top-half finishes in Serie B over the next two years, Magni joined Bari in 1962. The club won promotion to Serie A during his first season in charge. Magni left the club in 1963 and spent the next two years away from management. He returned to Varese in 1965, who were now a Serie A club. The club finished bottom of the table during the 1965–66 season and were relegated. He joined Pavia in 1966 and managed them for a season before spending another two years away from the job. He finished his managerial career with a brief stint at Serie C side Salernitana in 1969.