 Saputo became chairman of the board and president of Saputo Inc. in 1969, and he was named chairman and chief executive officer (CEO) in 1997 when the company went public.In March 2004, his son Lino Saputo Jr. was appointed to the position of president and CEO, while Saputo continued as the company's chairman.In August 2017, Lino Saputo Jr. assumed the role of chairman, and Saputo remains the majority shareholder of Saputo Inc.

Possible links to the Mafia have been raised in the past, more recently in January 2020 with Radio-Canada investigative program Enquete.