Archduchess Maria Anna Josepha was born on 30 December 1654 as the third child and daughter of Ferdinand III, Holy Roman Emperor (1608–1657) and his third wife, Eleonora Gonzaga (1630–1686).

Two months after she was born, her eldest full sibling, Archduchess Theresa Maria Josepha (1652–1653) died at the age of one and a half years.

On 25 October 1678, twenty-four-years-old Maria Anna married twenty-years-old Electoral Prince Johann Wilhelm (John William) (1658–1716) from the House of Wittelsbach in Wiener Neustadt.

[4] Upon Philip William's death, Johann Wilhelm became Elector Palatine and Duke of Neuburg.

She was buried there in the Imperial Crypt beneath the Capuchin Church, the principal place of burial for members of the House of Habsburg.