Aubery was born the son of Jehan Aubery du Maurier and his second wife Madeleine Froger. His parents were both huguenots. He was therefore also raised in that faith. He studied in Le Mans, and after 1582 in Paris at several colleges, among which the "Collège de Clermont". He studied philosophy under Theodore Beza for a year after 1583 in the Republic of Geneva. He was destined for a career in the "noblesse de robe", because a great-uncle (Jacques Aubery) was an advocate before the "parlement de Paris" during the reign of Henry II of France. (He took part in the prosecution of the perpetrators of the Mérindol massacre.). But the events of the French religious troubles intervened. In 1585 (a year after his father died) the huguenots were given six months to convert to Roman Catholicism or to go into exile. Aubery decided to join the army of the prince of Condé and took part in the Battle of Coutras under Navarre in 1587. From there his career took flight.