There's an unused firefly sprite which appears similar to the Beehive's Bee sprite which even uses the same wings. It's possible this was intended to be used for the world Mad Monster Mansion, the only level set during night.

In the original Nintendo 64 version, if you input too many "illegal" cheats in the sandcastle in Treasure Trove Cove, Gruntilda will permanently delete your save file. This won't come into effect until you have saved and quit or turned off the console though.

In the Xbox Live Arcade version, entering any cheat except for those given by Cheato and Bottles will disable saving for the current playthrough and remove the player's score from the leaderboard. Oddly enough, there is no penalty for inputting too many cheat codes in this version, even though all the text about erasing the save file is retained. This was fixed in the 2026 Evercade port of the game.

When you collect a Mumbo Token, a sound effect of Mumbo saying "Ikkum Bokum" plays. This phrase (and most of Mumbo's speech aside from "Oominaka" and a few other sound effects) are all made up of randomly-arranged soundbites. When these soundbites are arranged in the correct order, they say "Come and have a go, if you think you're hard enough."

When Mumbo turns you into a creature he says "Oominaka." Grant Kirkhope, Mumbo's voice actor, revealed that at the time of recording the voices for the game his left testicle was swollen. "Knackers" is British slang for testicles, so he thought it would be funny if Mumbo said "Ooh, my Knackers." Thus, every time that Mumbo uses his magic to turn you into a creature, he's actually complaining that his testicles are in pain.

The music played inside the Ant Hill of Mumbo's Mountain is a slowed down version of what was originally intended to be the world's main theme. The original theme was partially inspired by the Baby Elephant Walk tune from the film "Hatari!".

The theme that was used for the world Treasure Trove Cove was also the second version that the game's composer, Grant Kirkhope, had written due to the change of the game from "Project Dream" to "Banjo-Kazooie".

Napper the Ghost and Clanker's voices are both Banjo's voice but slowed down and lowered respectively. This was done due to not enough memory space on the cartridge to add additional voices.

On the third file select, you can see Banjo and Kazooie playing a Game Boy. The sound effects coming from the Game Boy are from Donkey Kong Land. Oddly enough this would still be featured in the Xbox Live Arcade version. In the 2026 Evercade version however, the Game Boy would be replaced with Evercade's Rare-themed Super Pocket handheld console.

On the title screen, there is a slight chance that you may get an alternate file select animation. These include Banjo being flipped out of his bed and out his window, the wall in Banjo's kitchen spinning around, and Banjo being launched out of his chair.

A few of Banjo-Tooie's worlds were originally planned for its predecessor, Banjo-Kazooie, such as the fire side of Hailfire Peaks and Glitter Gulch Mine. Many of these were cut primarily because of time constraints.

Gobi mentions leaving for the "Lava World" in Click Clock Woods, which adds up as Gregg Mayles' concept art for the cut lava world shows that Gobi would have been present. Gobi would eventually live up to his promise by appearing in the fire side of Hailfire Peaks in Banjo-Tooie, after being freed in Witchyworld.