Prior to the film's release, it was originally announced that this would be the final Spy Kids movie, as the young actors, in particular Alexa PenaVega were literally growing out of the role. However eight years later, Spy Kids: All the Time in the World in 4D (2011) was released which featured Alexa Vega and Daryl Sabara in supporting roles.
When Juni and Grandpa emerge from the game, Grandpa says that the armrests on his wheelchair are covered in rich Corinthian leather. This is a reference to actor Ricardo Montalban's Chrysler Cordoba television commercials in the late 1970s ("The seats are upholstered in rich Corinthian leather").
The HD/3-D process is the same used by director James Cameron for his IMAX feature Ghosts of the Abyss (2003), although the projection is different. Cameron used polarized projection only viewable in special venues. Rodriguez used the traditional anaglyph (notable for its scarlet red and cyan blue lensed glasses) projection. The cameras used for the film consisted of two custom-designed Sony HDC-950 cameras (HDCAM) which have had their image sensors separated from the main body of the camera and rehoused 70mm apart - the same distance between a pair of human eyes. This also allowed director Robert Rodriguez to view immediate 3D playback on-set.
In Italy, for the theatrical release, the film was renamed simply "Missione 3-D: Game Over" ("3-D Mission: Game Over"), without any references in the trailers, or anywhere else, to its being a part of the Spy Kids franchise.
During the climax of the film when Juni is destroying the Toymaker's creations, one of Toymaker's henchmen says "That's kid's like Rambo" and the camera shows a shot of Toymaker giving a snarl look. This is a reference to the Rambo franchise where Toymaker (Sylvester Stallone) plays the former green beret who never draws first blood.
Elijah Wood: Robert Rodriguez wrote the role of 'The Guy' with him in mind. Wood had previously starred in Rodriguez's The Faculty (1998) shortly before finding out about The Lord of the Rings: The Fellowship of the Ring (2001). The suit that Wood wore was originally one for the character Juni, but they spray-painted it silver and Cellotaped it to him as it barely fit. In the shot where Wood is kneeling down, talking to the others, he is actually looking at the ground to give the impression that he is towering over everybody.