In the Challenge of Atlas, after having both Hades and Zeus' Shields, head past the room with the wall spikes and across the bridge. Just before the ladder, a harpy will spawn. Attempting to lure the harpy next to the ladder and killing it will cause it to infinitely produce red orbs for its death. The amount of reds rewarded from this glitch varies from 20,000 to 60,000 orbs.

Hitting R2 in the following spots in the Temple of the Oracle will cause a message to appear in the sky:
• The top left corner of the map next to a red orb chest and what appears to be human feces.
• On top of the Gravedigger's dirt pile.
• Between the two pillars of fire at the entrance.

The message will read: "Surrender Kratos"

In the PAL release, the sacrificed soldier found in the Chamber of Poseidon is replaced with an undead legionnaire.

The game's developers described the gameplay as "merging the action of Devil May Cry with the puzzle-solving of Ico".

Director David Jaffe wanted the game to have a fairy companion, similar to Navi in The Legend of Zelda: Ocarina of Time. The fairy would accompany Kratos, but halfway through the first level, he would have grown annoyed with the fairy and killed it. This idea was ultimately scrapped.

In the PS3 re-release, it's possible to obtain a trophy called "Speed of Jason McDonald," which is obtained for beating the game in under 5 hours. The trophy is named after Jason McDonald, the Senior Combat Designer for God of War III, who held the office record for the best speed-run for God of War.

In the North American release of the game, upon completing God Mode, you are rewarded with a phone number (1-800-613-8840). Calling this number will play a message from Kratos, in which he congratulates the player and reveals the true fate of Ares following the events of the game, and hints at another secret that can be found.

This secret involves two statues that appear at the end of the game. If you strike them, nothing happens to tell you they are of any significance, but if you keep hitting them somewhere between 200 to 400 times, they will finally break. A cutscene with a scrambled code will appear on screen. Decoding it reveals another phone number (1-888-447-5594). Calling this number will put you through to Kratos who again congratulates the player, before being interrupted by David Jaffe, the game's director. Kratos eventually gets fed up trying to understand his talk of video games and kills him, ending the call.

In the international releases of the game, these secret messages are not available through phone numbers due to regional restrictions. The first message is included via a cutscene with scrolling text rather than the original audio, while the second message showcases the original audio in higher quality.

As of 2022, both phone numbers are still in use for these Easter eggs.

During development, the Cyclopes had visible penises. This matched up with other creatures having bare breasts and nipples. The reason behind this was the game's creator, David Jaffe, wanted the creatures to come across as wild animals.