In his early concept art, Taven was supposed to have a bow as a weapon. However, this was cut from the game due to his fireball attack being more effective.

John Vogal explained on his twitter that although they originally planned for Taven to be the one to defeat Blaze, in the sequel it turns out to be Shao Kahn, making Taven's ending non-canon.

One of Sektor's Pulseblades moves is called Ketchup's Revenge. This is a reference to Sektor's placeholder name in Mortal Kombat 3, Ketchup.

There are a number of references to various anime series and video games in the Kreate-A-Fighter mode. These include Dragon-Ball Z, Sailor Moon, Street Fighter, Final Fantasy and Gatchaman.

Video Game Activist Jack Thompson tried to get Mortal Kombat: Armageddon pulled off of the shelves when it was released. Players were using the Kreate-A-Fighter mode to make a character with Jack Thompson's likeness and he felt that his image was being used without his permission. Armageddon was not pulled off the shelves and became one of the best selling games of 2006.

In the official wallpaper for the game, Stryker can be seen in his MK3 outfit, even though it was never shown in-game.

During development, Daegon was codenamed Doug until he was given his actual name.