Might be stretching it, but Eternal Darkness has several chapters set in a French cathedral and one of said chapters focuses on the Franciscan monk protagonist getting framed for murder of a fellow monk there.

Oh and I just remembered Immortality has one of its movies be an adaption of the novel, The Monk, which is about a pious monk's descent into debauchery and murder.

Alright last one and I'm done because I don't want to keep spamming the comments, but Fire Emblem: Three Houses would count too. It's not the main focus of the plot as a whole, but an early arc in the game is investigating The Death Knight supposedly kidnapping and killing people on the Garreg Mach monastery grounds. You later find out there is actually some murders going on.

@ZapRowsdower Thank you for the suggestions.