Humbert was shortly repatriated in a prisoner exchange and appointed in succession to the armies of Mainz, the Danube and Helvetia, with which he served at the Second Battle of Zurich. He then embarked on an expedition to Saint-Domingue, which was in the midst of a slave rebellion, to restore French control over the colony and reestablish slavery. Humbert was accused of looting in Saint-Domingue by Jean Baptiste Brunet, and was also rumored to be having an affair with Pauline Bonaparte, the wife of his commanding officer Charles Leclerc. He was sent back to France by order of Leclerc in October 1802, for "prevarications, and liaison relationships with organisers of the inhabitants and with leaders of brigands". A committed republican, his displeasure at Napoleon's imperial pretensions led to him being dismissed in 1803 and he retired to Morbihan, Brittany.