The idea for The Talos Principle first spawned from the development of Serious Sam 4; developers Croteam were experimenting with the use of interactive objects as part of the game design while creating levels that fit within the Serious Sam design style. This led to some complicated puzzles that they were inspired to build upon further as a separate title, as they felt players wouldn't like puzzles in a Serious Sam game.

In Area B: Room 2, during the puzzle "Moonshot", a tiny connector can barely be seen on the texture of the Moon. By hitting the connector with the red laser, the Moon will begin to rotate until the dark side of the Moon comes into view. The bright symbol seen on the face of the Moon is the Aperture Science logo from the Portal series. However, another small white speck can be seen on the very top of the logo.

Afterwards, in the puzzle "Man on The Moon", after launching yourself over to the forcefield, you can find a small key hidden just to the right of it. After returning to the other side of the wall, use the far-most fan to launch yourself onto the arches to the left, and then maneuver your way to a viewfinder that is unlocked by the small key. The viewfinder allows you to get a better look at the speck on the Moon, which is revealed to be Wheatley from Portal 2 staring back at you, in reference to that game's ending where Spoiler:Wheatley is sucked into a portal on the surface of the Moon.

In Area B: Room 5, it is possible to reach the top of the building just above the teleporter that brought you there in the first place. To do this, you must go to the puzzle "Behind the Iron Curtain" and while completing it, maneuver your way so that a box and fan used in the puzzle are blown out of the puzzle's walls into the Room's map. Afterwards, take the box to a nearby hole that leads to the river until you find a connector for the fan and place it there. After going back to retrieve and place the fan, jumping into it will blast you through the air across the map and onto the top of the building, which will then suddenly teleport you to a dark cave. Walking further into the cave will reveal a glass pyramid prism with a light shining through to create a rainbow. This is a recreation of the cover art of the band Pink Floyd's 1973 album "The Dark Side of the Moon", and interacting with the prism will play a short cover of the instrumental opening to the first part of the song "Shine On You Crazy Diamond" from Pink Floyd's 1975 album "Wish You Were Here".