During development, the first boss fight the developers planned for the end of each set of stages was a giant flying squirrel named Momogaa, or simply "The Giant Squirrel" in English (according to an issue of Nintendo Power magazine). The Giant Squirrel would fly around and drop nuts that Mario could then throw back at it, and was roughly 1.5 times the size of Donkey Kong. This size difference, on top of it being the first boss, were the reasons it was scrapped from the final game, as it made Donkey Kong seem less threatening in comparison. The Giant Squirrel would briefly see use as a villain in Kodansha Comics' Super Mario manga in 1995, in which it leads an army of Kremlings from Donkey Kong Country against the protagonists of both games in retribution for being cut from the Game Boy game.

The game opens with remakes of all four levels from the original 1981 Donkey Kong arcade game. These are not direct remakes of the original levels; they were made easier and some of the stage designs had to be scaled back to fit the Game Boy's smaller screen. There was a back and forth argument within the development team over where to place these levels in the new game, as they did not want it to be mistaken for a remake. While they initially planned to make the original levels post-game content, they were ultimately placed at the start of the game. According to director Takao Shimizu, this placement was not intended to give players expecting a remake a surprise (akin to a "bait & switch"), but was rather meant to cater to nostalgic fans of the original Donkey Kong.

This was the first Game Boy title designed with enhanced features when played on the Super Game Boy. Playing this way added a set value of colors and a background that looked like the Donkey Kong arcade cabinet.