After the death of Pope Paul IV, he moved to his diocese of Piacenza where he repressed any Protestant dissent.

Returning from Germany, he moved to Venice where he was appointed Prior of the Theatine house at Tolentini's church.

[1] In 1555, Pope Paul IV, one of the founders of the Theatine Order, summoned Scotti to Rome, making him Archbishop of Trani and cardinal priest in the consistory of 20 December 1555.

[2] In Rome under Paul IV he cooperated to the preparation of the Index Librorum Prohibitorum and in drafting the new Breviary.

Scotti therefore decided to move from Rome in his new diocese,[2] after having been consecrated bishop on 25 April 1560 by Cardinal Jean Suau.