It was originally intended for both parts of Metal Gear Solid V, Ground Zeroes and The Phantom Pain, to be a single game, but the game's designer, Hideo Kojima, wanted people to experience the game near the launch of the recently announced next generation of consoles (PlayStation 4 and Xbox One). Ground Zeroes was also considered for the PlayStation Portable, but development proved to be much tougher than expected, and that version was cancelled.

However, in 2023, Kojima stated on Twitter that he originally intended for Ground Zeroes to not just be released separately as a prologue to The Phantom Pain all along, but he also intended it to be the first installment of an episodic series. His reasoning for this was due to lengthy development times for recent games resulting in ideas changing over the course of production. His original plan was to produce the first episode to gauge audience reactions, and then develop two more episodes while receiving feedback, but due to criticism over the game's short length and pricing, and subsequent confusion over whether or not Ground Zeroes was considered a full game, this plan was scrapped.

In the side op Intel Operative Rescue, the player has to help an agent get into the helicopter. In the end cutscene, he is revealed as the creator of the Metal Gear series, Hideo Kojima. After the mission, he'll be in the helicopter in the main menu and waiting a while on the mission select screen will make him spin the list of missions.

In an early draft of the game's story, it was intended for Paz's dead body to be lying in the cage next to Chico, thus leaving him to watch her corpse gradually decompose over time.

During the Deja Vu extra mission in the PlayStation 4 release, interacting with the prisoners in Chico and Paz's cells will cause both prisoners to die from Foxdie. After both prisoners are dead, the Fox Engine will appear to be under attack, and will then correct itself moments later.

In international versions, there's a cutscene of removing the bomb from inside of Paz's stomach at the end of the main mission. The Japanese version however adjusts the camera angle so that no blood and gore is shown on screen.