Flaget left Baltimore with two colleagues in 1798 bound for Cuba as part of a Sulpician mission to establish a college on that island. They were met with opposition from the local diocesan administrators, however, and were not able to celebrate Mass in Havana. During that stay, he contracted yellow fever and was left behind when the other Sulpicians decided to return to the United States. He recovered and acted as a tutor to the son of a wealthy Spaniard. Later, after the death of the Archbishop of Havana, the Dean of the Cathedral granted him permission to celebrate Mass at the church of the Capuchin friars. Flaget learned Spanish during his stay. While he was in Cuba, Louis Phillippe of France and his two brothers had arrived there on their journey in exile. The refugee aristocrats were befriended by their fellow Frenchman, Flaget, in 1800. This was a kindness which Louis Phillippe remembered and returned when he later ascended the throne of France as King.