In 1655 he returned to France. Not long after he was appointed director general of the company; but having again returned to Madagascar, he was drowned on his voyage home on the 10th of June 1660. He is the author of a Histoire de la Grande Isle Madagascar (1st edition 1658, 2nd edition 1661), which included one of the first descriptions of a game similar to Bao. Flacourt was one of the few, if not the only, Western person to have recorded knowledge of the elephant bird of Madagascar when they were possibly still extant.