His pious sobriety was influenced by his friendship with Cardinal Gabriele Paleotti of Bologna, who had attended the Council of Trent.

After his return in 1591, one of his project was a series of frescoes on the Passion of Christ for the Carthusian Monastery (Charterhouse) or San Girolamo in Bologna.

In 1595, Cesi completed the triptych including the 'Adoration of the Magi and Virgin and Saints for the Basilica of San Domenico in Bologna.

[2] Cesi was inspired by the Counter Reformation's interest in education and the use of art as a vehicle for renewing faith and promoting the Roman Catholic creed.

Three versions of a Crucifixion with saints (1585–1600) of which one made for an altar in the church San Martino, Bologna, show his mature style: sober mood and intellectual and abstract composition and naturalistic figures.