Spyro: Enter the Dragonfly's villain was originally going to be a dragon, but the lead designer was adamant that the Spyro universe could not have any evil dragons. Ironically, the following release Spyro: A Hero's Tail would introduce Red, an evil dragon.

In the prototype version of the game, Blink's hat is red as opposed to purple in the final.

Hogwarts can be found hidden in the game files. EuroCom also developed a Harry Potter game, so it was likely imported to test Sgt. Byrd's flight mechanics.

Mrs. Shoutfire's name is a reference to the character Mrs. Doubtfire from the film of the same name.

Utilizing a glitch that allows the player to swim in mid-air, while in Coastal Remains it is possible to see an unfinished building floating in mid-air.

The Dragon Elders Tomas, Magnus, Titan and Astor are all based on characters from the first Spyro game. However, their appearances have been dramatically altered.

There are several references to the Mario franchise througout the game:

•When attempting to activate the ball gadget, The Professor mentions two signature items in the Super Mario series, Power Stars and Red Coins, when trying to recall the name of a valued collectible, the Light Gems. Not only this, but he mentions Heart Pieces as well, which is a reference to a collectible found in The Legend of Zelda series.

•There is a robot NPC named Mergatroid found in Red's Laboratory who wears a red shirt, blue overalls, and a red cap with the letter "M" on it.

•There is an enemy type in Crocovile Swamp that resembles a Piranha Plant. A variation of this enemy also spits fireballs, much like a Venus Fire Trap.

•Lastly, there are hostile Yetis in Gloomy Glacier who throw barrels, similar to Donkey Kong.