The church was nearly ruined at the time of archbishop Charles Borromeo (1560–1584). Later it was abandoned and used as peasants' store and lost the small right aisle in a fire. Other sections went lost during the French occupation in the early 19th century, when they were considered of no artistic interest and sold to private collectors. The basilica was acquired by the "comune" of Cantù in 1909 and restored in 1933–1934.