Preceded by the execution of the large fresco with the Tree of Jesse laid out in 1556-1562 by Giuseppe Arcimboldi and Giuseppe Meda on the head of the southern transept, a new phase of work began from the years of the episcopate of San Carlo Borromeo (1563-84). In accordance with the archbishop’s prescriptions, in 1575-1577 Pellegrino Tibaldi rebuilt the choir, under which a vast crypt was excavated in 1611-14.
To the author of the latter, Ercole Turati, we owe also the colossal bell tower, erected in forty years of work starting from 1592, and the new baptismal font (1620-22).
In 1681, a large octagonal chapel was built next to the sacristy for the Treasury.
With the transfer in 1648 of the feud of Monza to the Durini counts, a series of new decorative campaigns also began, intended to define that characteristic baroque face that today dominates the interior layout of the building.
Inaugurated by the frescoes laid between 1648 and 1663 on the walls of the major chapel by Stefano Montalto, Ercole Procaccini the Younger, Isidoro Bianchi and Carlo Cane, the decorative campaigns continued until 1753 in the naves and chapels, Involving some of the greatest painters of Lombardy at that time, from Legnanino to Borroni, from Castellino to Carloni.
In 1792-98 Andrea Appiani finally built a new high altar, replacing the one, now dilapidated, created in 1590 by Rizzardo Taurino.
