Her maternal grandparents were Archduke Ferdinand of Austria-Este and Maria Beatrice Ricciarda d'Este. Ferdinand was the fourteenth child and third son born to Francis I, Holy Roman Emperor and Maria Theresa of Austria. Maria Beatrice was the eldest daughter of Ercole III d'Este and Maria Theresa Cybo, Princess of Carrera.
On June 20, 1812, Maria Beatrice married her maternal uncle Francis, Archduke of Austria-Este; the couple received a special dispensation for their marriage from Pope Pius VII. Maria Beatrice's husband became Francis IV, Duke of Modena, Reggio, and Mirandola on July 14, 1814. They were parents to four children:
With the death of her father on January 10, 1824, Maria Beatrice became recognized by Jacobites as "Mary III, Queen of England, France and Ireland" and as "Mary II, Queen of Scotland". The regnal numbers in England are a reference to her descent from Henrietta 'Minette' Stuart, Duchess of Orleans, youngest daughter of Charles I of England. After the death of the last of the Jacobite 'Pretenders', Henrietta's line-through her younger daughter (Anne-Marie of Orleans, wife of Victor Amadeus II of Savoy) became the sole legitimate line of descent of Charles I, and therefore superior to the Hanoverian claim which was based on descent from Charles I's sister Elizabeth. Maria Beatrice never actively pursued her British claims.
Maria Beatrice died of a heart condition on September 15, 1840. Her son Francis was the next Jacobite pretender.