The appearance of the plague at Padua obliged him to retire to his native city. Shortly afterwards he was called to act as tutor to Ferrante (Ferdinand) Gonzaga, from whom he received the rich abbey of Guastalla. He held office as abbot for 25 years, and then retired to his native town. In 1612 he was employed by the duke as his envoy to Venice. Baldi died at Urbino on October 12 1617.
He is said to have written upwards of a hundred different works, the chief part of which have remained unpublished. His various works show his abilities as a theologian, mathematician, geographer, antiquary, historian and poet. The Cronica dei Matematici (published at Urbino in 1707) is an abridgment of a larger work, on which he had bestowed twelve years of labour, and which was intended to contain the lives of more than two hundred mathematicians. His life has been written by Affô, Mazzuchelli and others.