The couple had only one child, Princess Anna Beatrice (19 October 1848 in Gries, Bolzano – 8 July 1849 in Modena).

As member of a cadet branch of the House of Habsburg-Lorraine he also bore the titles of an Archduke of Austria and a Prince Royal of Hungary and Bohemia from birth; from his father he inherited also the titles of Duke of Reggio and Mirandola, Duke of Massa, Prince of Carrara and Lunigiana.

At the death of his cousin the Duchess Marie-Louise of Parma on 18 December 1847, he succeeded as Duke of Guastalla.

During the revolutions of 1848, Francis was forced to flee his duchy by a popular uprising and was restored by Austrian troops in the following year.

On 18 March 1860, King Victor Emanuel II of Sardinia ordered Modena to be incorporated into the new Kingdom of Italy.

Constantine Phipps, Marquis of Normanby published a book later that year rebutting all of Gladstone's charges against Francis.