François Ier d'Autriche
Marie Anne was buried at the Capuchin Church in Vienna, more specifically in the Imperial Crypt, the burial place of her siblings Marie Louise, Duchess of Parma, Ferdinand I of Austria, Archduchess Marie Caroline, Archduchess Caroline Ludovika of Austria, Archduke Johann Nepomuk of Austria, Archduchess Amalie Theresa of Austria, and Archduke Franz Karl of Austria. Her parents, Francis II, Holy Roman Emperor and Maria Theresa of Naples and Sicily, and her great-grandmother, Maria Theresa of Austria, are also buried there.