As the younger son of a seigneur in an intensely religious family of bishops and soldiers,[3] he was destined for a career in the church.
He studied in Toulouse, then at the Collège de Navarre, Paris, and received his doctorate degrees in canon and civil law at the University of Orléans.
On 16 February 1587 he was appointed by Henry III French minister to the Holy See, cardinal protector of France;[8] he retained his predecessor's secretary, Arnaud d'Ossat, a skilled diplomat with long experience in Rome who served as liaison with the papacy during Joyeuse's numerous absences.
Reappointed cardinal protector in January 1596, he returned to France and was returned to Rome by Henry IV in September 1598, arriving the following February; that year he negotiated the annulment of King Henry's marriage to Marguerite de Valois, opening the way for a second marriage to Marie de' Medici.
Between 1606 and 1607 he played a decisive role in negotiating a rapprochement between the Papacy and Venice, at the time of the Venetian Interdict.