Captured by English forces in 1746, he was held as a prisoner of war until the Treaty of Aix-la-Chapelle set him free, whereupon he returned to working in the French naval bureaucracy.

In February 1763, Jean-Jacques d'Abbadie was commissioned director-general of Louisiana (New France), a position formed by consolidating the former governor and ordonnateur roles.

He was charged with the responsibility of dismantling the French garrison and preparing the colony for occupation by English and Spanish forces, pursuant to the terms of the Treaty of Paris (1763).

He traveled to Mobile to assist British forces in assuming control in West Florida and to supervise the transfer of the region's French soldiers to French-held territory.

D'Abbadie was criticized by New Orleans merchants for favoring the Laclède-Chouteau interests with exclusive Indian trading privileges in Upper Louisiana.