Visconti, who was of pleaser and feeble nature, was not able to oppose to the commands of the religious reforms of Joseph II: in particular he accepted the expropriation of the Valsolda's tenure and of the Collegio Elvetico which belonged to the Diocese of Milan, the closing of the historical seminaries founded by Saint Charles Borromeo with the opening of a single seminary in Pavia under the control of the government and near to Jansenism positions, the reduction of the parishes (25 December 1787) of the monasteries and of the confraternities, the new law on the marriages which moved them under the State's law and the broad reduction of jurisdiction of the ecclesiastic tribunals.

[1] With the death of Joseph II in 1790 the situation of the Church in Milan slowly improved, the seminaries were re-established, and Visconti re-published the Ambrosian Missal and issue a new text of Christian Doctrine.

The population reacted with riots, particularly in Binasco and Pavia, and Visconti, to please the new ruler, tried to calm the turmoils and ordered prayers in all churches in favour of the army of the French First Republic.

[3] A brief break occurred between 1799 and 1800 when the Austrians returned in Milan for a few months: Visconti openly rejoiced for the change of rulers who revoked some of the anticlerical measures.

Returned in Milan in November 1800, he made himself available to the Cisalpine Republic, which restored its repressive rules against the Church and against the religious sentiment of the population.