Abbe Baudoin studied at the college of Nantes at first, taking up a military career and becoming a musketeer in the king's guards. He became a priest in 1685. He was a missionary in Acadia where he arrived in 1688. From Port Royal he soon moved to Beaubassin, where together with the Sulpician Claude Trouve he carried on his priestly duties in the farthermost reaches of the Baie Francaise (Bay of Fundy). He occasionally took part in Indian expeditions against New England.
During his stay in Acadia, Baudoin was accused of exerting undue influence in civil matters, and he clashed with Governor Joseph Robinau de Villebon. In this connection a stern letter from Versailles required him to go to France with Bishop St. Vallier in the fall of 1694 in order to exonerate himself. He returned in the spring of 1696 with Pierre Le Moyne d'Iberville who was entrusted with an expedition against the English. Abbe Baudoin accompanied him both as chaplain and as an expert on Acadian problems. He thus took part in the capture of Pemaquid and in the conquest of Newfoundland, leaving a detailed diary of the whole expedition. He returned exhausted to his mission at Beaubassin and died there towards the end of the summer of 1698.