Not with standing the fact that all things were well in place, a difficult political period began. We can say that the last years of Msgr. Lartigue's episcopate were among the most painful of his life. They coincided with the crisis that shook Lower Canada: The Troubles of 1837 - 1838 and their consequences. A confrontation was brewing between the Patriots and the British government in power. From his cathedral on July 25, 1837, the Bishop of Montreal cautioned the faithful of his diocese against any revolutionary action. For two days, more than twelve hundred Patriotes marched in front of Saint-Jacques cathedral to contest the Bishop's directives. Not allowing himself to be intimidated, Msgr. Lartigue addressed his diocesan priests on October 24th to protect them against the rebels' speeches and threats. He reminded everyone of their duty to legitimately established authority, he evoked the horrors of a civil war and the bloodthirsty character of any popular revolution.

The Patriots did not hesitate to describe this proclamation as “anti-reason”, even “anti-Catholic”, accusing the bishop of seeking to win the favour of the authorities, of having ignored the misfortunes of his people, and of being insensitive to their temporal and spiritual miseries...

On January 8, 1838, Msgr. Lartigue  came with a second call in which he asked his diocesan brothers in particular: "What must you think today (after the fighting and the destruction of the autumn) of your clergy who made every effort to protect you against perverse doctrines, who even incurred the hatred of many, because they did not speak to you in the sense of a faction in which, unfortunately, some of you were engulfed at the time..."

It is understood that Msgr. Lartigue's attitude was based on two considerations: the legitimacy of political power, which is of divine origin as theology then advocated, and the inequality of the forces involved; that is, the militarily under-equipped rebel patriots on the one hand, and the abundant resources of the English army on the other. The Patriotes' record: one victory, several defeats; many deaths, the children and fathers of families; brutal reprisals (burned villages, scorched earth strategies, incarceration of the defeated...).

Lartigue had tried to remain calm in the midst of the turmoil. History would prove him right. The revolution ended in considerable failure. In warning his compatriots against a patricidal and unequal struggle, Lartigue had shown a political flair and wisdom that many took note of, especially the moderate Patriotes of the Quebec region.