Although he graduated with a medical certificate there in October 1831, he was at first not allowed to practice in Lower Canada because he had completed his studies in less than five years.
Côté became a leader for the Patriote movement in his region and joined Les Fils de la Liberté.
Although originally supporting Louis-Joseph Papineau, he now allied himself with Robert Nelson and helped prepare a declaration of independence for Lower Canada.
The American authorities arrested the group's leaders because the United States were officially neutral in this dispute but they were released shortly afterwards.
In 1848, he went to Philadelphia and helped prepare pamphlets to educate people about the Baptist faith, as well as translating an existing work into French.