Eleonora spent her childhood at the court of Mantua. Famous for her singular beauty, she married Ferdinand in Innsbruck on February 2, 1622, whose previous wife Maria Anna of Bavaria had died in 1616. But the family Gonzaga did not — as expected — profit from this connection, because some counsellors of Ferdinand declined this marriage. The troops of the Emperor even captured and destroyed the capital Mantua in the War of the Mantuan Succession (in 1630).
The papal Nuncio Caraffa described Eleonora not only as beautiful but also as pious. For example she established Carmeliteconvents in both Graz and Vienna.
The royal couple had no children, but Eleonora became stepmother to Ferdinand's four surviving children from his previous marriage.
Eleonora died in Vienna in 1655 and was first buried in the Carmelite convent of the Austrian capital until her body was transported in 1782 into the St. Stephen's Cathedral of the same city.