Born in Regensburg, Eleonore was the daughter of Holy Roman Emperor Ferdinand III and his wife, Eleonora of Mantua.

The pro-French opposition party under the leadership of John III Sobieski and Mikołaj Prażmowski attempted to convince her to divorce, but she refused and instead demonstrated loyalty toward the king.

[2][3] Queen and Grand Duchess Eleonore was regarded as an ideal model of a good, supportive and loyal spouse.

In February 1672, the queen was asked to act as a mediator between King-Grand Duke Michael and the opposition leader John III Sobieski during the 1672 Sejm.

[2][3] She accepted the assignment and entered negotiations assisted by the papal nuncio Franciszek Buonvisim, the bishop of Kraków, Andrzej Trzebicki, and the voivode of Vitebsk Jan Antoni Chrapowicki.

When she married Charles, there were fears in the Commonwealth that she was planning to overthrow King and Grand Duke John III Sobieski and install her own spouse as a ruler.

[2][3] Eleonora did keep in contact with pro-Habsburg Polish magnates such as Dymitr Jerzy Wiśniowiecki, Kalisz Voivode and Jan Karol Opaliński, but no such plan was ever realised.