His pastoral letter of 1905 (The Church and the new times) was clamorous, following the French anti-clerical law in which the separation between State and Church was sanctioned: in contrast to the Holy See, which, following the law, intervened with several encyclicals of condemns and broke diplomatic relations with France, Geremia Bonomelli argued that the Church separated from the state would enjoy greater freedom. Following the publication of this pastoral letter, an apostolic visitor accused the bishop of favoring modernism in his diocese. Bonomelli justified himself with anti-modernist declarations.
Don Primo Mazzolari, his disciple, who risked to pay with his life his intransigence against every abuse, he called him "a man of unbearable greatness from our imbecile times [...] a bishop of his time, did not stop to see pass the transformations of his time in which he lived, but he boldly climbed on the convoy ».
Mons. Geremia Bonomelli died on August 3, 1914. He rests in the Cathedral of Cremona in a sarcophagus next to the main altar.