[2] In 2006, Alain Simoneau, an atheist who regularly attended council meetings, asked Tremblay to stop the prayers, claiming that they infringed on his freedom of conscience.

[13] The determination of whether the prayer was religious, whether it violated Simoneau's freedom of conscience and was discriminatory, and whether the expert evidence was admissible should be assessed using the reasonableness standard of review.

[14] Abella J supported instead a holistic approach that would consider whether the whole of a decision is reasonable or correct,[15] arguing that this would ensure a "principled and sustainable foundation" for the standard of review analysis.

[18] Gascon J held that "sponsorship of one religious tradition by the state in breach of its duty of neutrality amounts to discrimination against all other such traditions",[19] and that non-belief is equally protected under religious freedom, per R v Big M Drug Mart Ltd. Gascon J wrote that state neutrality is required so as to prevent discrimination, since a state-held belief would deny citizens' "equal worth".

Gascon J held that the Tribunal's finding that the prayer was religious in nature was reasonable, since the wording of the amended by-law demonstrated the City of Saguenay's support for the individual religions of the practicing councillors.

[25] Gascon J held also that the Tribunal's finding that the prayer amounted to an exclusion based on religion was reasonable, since it involved state actors practicing a religious act in the course of their duties.

[27] Finally, Gascon J held that Simoneau's rights to freedom of conscience and religion had been breached, since the "price for [non-participation]... was isolation, exclusion and stigmatization".

[31] Gascon J rejected further arguments by analogy to the prayer recited in the House of Commons of Canada, holding that there had not been sufficient evidence led to discuss the issue.

[32] Gascon J also dismissed the argument that the preamble to the Charter of Rights and Freedoms, which acknowledges that "Canada is founded upon principles that recognize the supremacy of God", had bearing on the issue.

Gascon J held that the preamble "cannot lead to an interpretation of freedom of conscience and religion that authorizes the state to consciously profess a theistic faith".

[33] Gascon J held that the Tribunal's decision rendering the by-law inoperable and ordering Saguenay council to stop recitation of the prayer was legitimate,[34] and that its imposition of $30,000 in compensatory and punitive damages was reasonable.