As Holy Roman Empress, she promoted the development of cultural and spiritual life at the Imperial court in Vienna, and despite being a staunch Catholic and benefactress of several monasteries, she had a tolerant attitude towards Protestantism.

The marriage of Eleonora's parents was made with the purpose to reinforce the claims of the Nevers branch of the House of Gonzaga to the duchies of Mantua and Montferrat when the main line would become extinct.

The princess received an excellent education, being fluent in French, Spanish and Italian, well versed in literature, music and art, and expert in dances and embroidery.

Duke Charles II agreed with only minor changes: Mantua would maintain its loyalty to the Holy Roman Empire only if the alliance didn't bring negative consequences to the duchy, and the bride's dowry would be paid in several installments in the next years.

[6] The marriage by proxy was solemnized on 2 March 1650 at the Basilica palatina di Santa Barbara, in which the emperor was represented by his ambassador, Count Johann Maximilian von Lamberg.

The cortege arrived at the Austrian city of Villach, where the bride said goodbye to her relatives and in the company of her godmother the dowager empress continued the trip to Wiener Neustadt, where on 30 April 1651 there took place the official wedding ceremony between Eleonora and Holy Roman Emperor Ferdinand III.

While her husband was engaged in public affairs, she was responsible for organizing celebrations such as the Carnival before Lent, culminating in the premiere of the opera L’Inganno d’amore (the Cheating of Love) by Antonio Bertali.

[6] Archduke Leopold Wilhelm, Ferdinand III's younger brother, thought to marry Eleonora (who enjoyed the respect of her subjects) to strengthen his position as a candidate for the Imperial crown.

There were often visitors like Minister Václav Eusebius František, Prince of Lobkowicz, ambassadors Jacques Bretel de Grémonville and Lorenzo Magalotti, and General Raimondo Montecuccoli.

For some time was considered the possibility of a second marriage for Eleonora, with the Polish King John II Casimir Vasa, but this project was never implemented.

The relationship with Leopold I's second wife Archduchess Claudia Felicitas of Austria were tense, but didn't last long due to her early death.

In 1669, Eleonora had to resolve the conflict between the Imperial court in Vienna and the Holy See, which arose due to the fact that the Pope didn't appoint any cardinal of the candidates proposed by the emperor.

[12][21][22] The last years of Eleonora's life were overshadowed by the epidemic of plague in 1679 and beginning of the Great Turkish War in 1683, in which, although the empire won, serious material damage was inflicted on the possessions of the dowager empress.