Eleonora spent her childhood at the ducal court in Mantua, which was one of the centers of European culture and science. When she was ten, her education was entrusted to her paternal aunt Margherita Gonzaga, Dowager Duchess of Ferrara and Modena, who, although she never took the veil, lived in a Clarissan monastery attached to the Church of Sant'Orsola, founded by herself. The Dowager Duchess saw to it that her niece received a good education, which included learning foreign languages, history, music and painting. The religious environment in which she grew up greatly influenced Eleonora, and was expressed in deeds of piety and charity.