The game is notable for two puzzles considered by fans and critics to respectively be one of the best and worst ever made for an adventure game.

The puzzle "Le Serpent Rouge" ("The Red Snake") involves decoding torn-up poem stanzas by hunting for information during the game and solving geometric mapping puzzles. This puzzle was widely praised for its overarching complexity and intriguing nature regardless of the player's interest in the real-life mysteries of Rennes-le-Château, a Southern French commune crucial to the game's plot that has been covered in various books and conspiracy theories. The poem was originally included in the "Secret Files of Henri Lobineau", a 1967 dossier about the fraternal organization the Priory of Sion, and was modified to make the puzzle solvable. Lead designer Jane Jensen named it her favorite and most challenging puzzle, designing it around the game's fully controllable 3D camera.

Meanwhile, a puzzle designed by producer Steven Hill was disliked internally and was meant to be replaced with a puzzle by Jensen, but time constraints forced it to be left in the game. It starts with Gabriel Knight finding that his friend Detective Mosely arrived in France the night before in a tour group and is scheduled to rent a motorcycle that day, so he goes to rent one himself. The nearsighted rental stand clerk requires a passport to confirm arrivals, revealing that the only rides he has left are a bike saved for Mosely and a cheap scooter. To get the bike, Knight plans to disguise as Mosely by Spoiler:stealing his coat and passport, and hiding his long blonde hair in a hat, despite putting it in a visible ponytail. He then draws a mustache on Mosely's passport photo to obscure their facial differences, goes to a shed, puts masking tape on a hole in the shed door, sprays a nearby cat with water causing it to run into the tape and stick fur to it, and applies it to his face with some maple syrup from breakfast to make a fake mustache. The disguise inexplicably works, and Knight gets the bike.

Moreso than Le Serpent Rouge was praised, the disguise puzzle was roundly criticized for its lack of hints, the impossibility of Knight convincingly impersonating Mosely, and the cartoonish roundabout way of Spoiler:making the mustache clashing with the game's serious tone. Critics felt that while it was not the most difficult puzzle, the solution was too absurd for the average player to think it would work. The most scathing review came from future Valve writer Eric Wolpaw, who blamed Jensen for the poor design (it was not known at the time that she did not design it), and called the process of Spoiler:making the mustache "deranged", controversially declaring it was proof that adventure games "committed suicide". While Jensen disliked the puzzle, she thought it being the death of adventure games was "kinda overblown", and the "length of the sequence and the lack of hints" was what made it bad.