His theological theories brought him into conflict in the French fort of Coligny (in present-day Rio de Janeiro), resulting in two Huguenots being expelled.
Cointac was aboard the second set of ships to reach France Antarctique, after Nicolas Durand de Villegaignon and his crew made the first successful voyage in November, 1555.
King Henry II, although Catholic, financially supported these voyages to the New World in an effort to avoid religious conflict at home and to expand his kingdom, though the Treaty of Tordesillas technically did not permit this colonization.
The second embarkation headed to France Antarctique was prepared under the name of King Henry II, under Bois-Lecompte, a nephew of Villegagnon, with 290 voyagers sailing on three ships.
Jean de Cointac was among a group of new arrivals who participated in theological debates in the new land, which eventually filled the fort with wranglings, factions, and feuds.