Born and raised as a Catholic, Eugénie grew up in the Palais Leuchtenberg on Ludwigstraße in Munich and frequently spent the summer months with her parents at Schloss Eugensberg, a castle built by her father on Lake Constance (at what is now Salenstein).

She remained childless and sought comfort in increasing piety, setting up an old-people's home in Hechingen and (in 1839) a major Kinderbewahranstalt for the town (the building which housed the latter contains a bust of her and is now the Amtsgericht).

Every Maundy Thursday, Eugénie and her husband washed the feet of twelve old and needy local people and then invited them to an Apostelmahl or Last Supper in the Billardhäuschen in the Fürstengarten, at which (after a grace) a stockfish with sauerkraut was passed round.

Her doctors gave her odd treatments, including the inhalation of fumes from cow dung and the burning of moxa sticks on her chest.

In summer 1847 she set off to seek a cure at the Badenweiler spa, but on the return journey she died at the Hotel Post in Freudenstadt on 1 September 1847.

On her mother's request, her heart was placed in an urn in the chapel of the Palais Leuchtenberg in Munich; since 1952 it has been housed in a niche beside the choir steps on the right side of the Stiftskirche.