In January 1859 she traveled to Vienna to spend time with her sister before they went to Trieste to formally enter her new kingdom, and say farewell to her family on the Neapolitan royal yacht Fulminante.

[2] Within the year, with the death of the king, her husband ascended to the throne as Francis II of the Two Sicilies, and Maria Sophie became queen of a realm that was shortly to be overwhelmed by the forces of Giuseppe Garibaldi and the Piedmontese army.

However, after that city had also been lost to the Garibaldines in the aftermath of the Battle of the Volturnus, he and Maria Sophie took refuge in the strong coastal fortress of Gaeta, 80 km north of Naples.

She was tireless in her efforts to rally the defenders, giving them her own food, caring for the wounded, and daring the attackers to come within range of the fortress cannon.

On 13 February 1861, the fortress capitulated, and thus the Kingdom of the Two Sicilies ceased to exist, effectively deposing Francis II and Maria Sophie.

With the fall of Gaeta and the Kingdom of the Two Sicilies, Maria Sophie and her husband went into exile in Rome, the capital of what for 1,000 years had been the sizeable Papal States, a large piece of central Italy but which, by 1860, had been reduced to the city of Rome, itself, as the armies of Victor Emanuel II came down from the north to join up with Garibaldi, the conqueror of the south.

[3] Countess Marie Larisch von Moennich, niece of Maria Sophie, had spread the story that the child's father was a Belgian officer of the papal guard named Count Armand de Lavaÿss.

Although Countess Larisch's biographer Brigitte Sokop refuted this assertion[4] and speculated that a possible father of the child would be the Spanish diplomat Salvador Bermúdez de Castro (later Duke of Ripalda and Santa Lucía),[5] who was often to be seen in the company of the Neapolitan royal couple and who was also said to have had an affair (and also an illegitimate daughter) with Maria Sophie's sister Mathilde, Countess of Trani,[6] Lorraine Kaltenbach established that the father of Maria Sophie's illegitimate daughter was indeed Félix-Emmanuel de Lavaÿsse, a pontifical zouave,[7][8] who officially recognized Daisy as his daughter on 16 May 1867[9][10] shortly before his death on 18 April 1868, aged 32.

Recent historians have resurrected that rumor based on the apparent credence given to this conspiracy theory by the then Prime Minister of Italy, Giovanni Giolitti.

Again, the rumors claimed she was involved in sabotage and espionage against Italy in the hope that an Italian defeat would tear the nation apart and that the kingdom of Naples would be restored.

Gabriele d'Annunzio called her the "stern little Bavarian eagle" and Marcel Proust spoke of the "soldier queen on the ramparts of Gaeta".