According to a "Rare Revealed" video released to coincide with Rare Replay, the boss character Lord Woo Fak Fak was named in reference to Rare engineer Paul Machacek, who would often swear whenever he found glitches in the code. When these issues were fixed, he would shout "Woo!", thus inspiring the boss' name.

Banjo-Tooie's Terrydactyland contains a sub area, dubbed the Stomping Plains, which in turn is home to the Stomponadon, a seemingly theropod dinosaur so enormous in scale that only its foot is visible. It functions as the main obstacle of this area as, hence its name, it will try to stomp on Banjo & Kazooie as they attempt to traverse the plains. The concept behind Stomponadon had its origins from Banjo-Kazooie's earliest prototype game, Dream: Land of Giants; footage of Dream released by Rare for the first time in 2015 showed that Edson (who was replaced by Banjo in the final game) was to have encountered a similarly large dinosaur that would try to crush him with its feet.

There was originally a mode called "Bottles' Revenge" which would allow for a second player to antagonize Player 1 in the main game. In it, the evil spirit of Bottles is able to free himself after being killed by Gruntilda. Whilst this mode is enabled, Player 2 can take control of a nearby enemy to attack Banjo and Kazooie. While this mode was cut from the game, it can still be accessed through the use of a cheat device. Devil Bottle's dialogue portrait also still appears in the Tower of Tragedy quiz game at the end. The mode would eventually see an official release in the 2026 Evercade port of the game.

On the sides of the Mumbo Pads, the words "eekum bokum" can be seen. These are part of what Mumbo chants while casting spells in the game.

Three of the characters in the game (Chris P Bacon, Old King Coal and Bullion Bill) were not actually named by Rare, but by members of the British public. Nintendo Official Magazine in the UK held a competition where the winners would receive a copy of the game once it hit shelves as well as a signed poster and their suggested name being used in the final game.

Washer Banjo, the transformation available in the Grunty Industries world, is a reference to the the first game in the series, where Mumbo might accidentally turn Banjo and Kazooie into a washing machine when casting a transformation spell on them.

Infamously, the ending cutscene of Banjo-Tooie has series antagonist Gruntilda threaten "Just you wait until Banjo-Threeie!". Contrary to popular belief, the lead designer for the Banjo-Kazooie series, Gregg Mayles, has stated that a direct sequel to Banjo-Tooie was never planned for development, and that the supposed "tease" was merely a joke, playing on how the word "Threeie" would be unpronounceable in British English. Instead, Banjo-Kazooie: Nuts and Bolts was actually the third attempt at creating a different kind of Banjo-Kazooie game to act as the third mainline installment in the series. The game initially began development as "Banjo X", a morphed "remake" of the first game for the original Xbox which featured some new assets and items. When development shifted to the Xbox 360, Mayles stated the game shifted to being about "an AI-controlled Grunty, who would be competing against Banjo in all the worlds". Around this time, development began on a kart racing title called Banjo-Kazoomie, which programmer Brendan Gunn reported working on for about two weeks. All of these builds were planned to incorporate multiplayer gameplay, but none of them made it far into development before being consolidated into what would become Banjo-Kazooie: Nuts and Bolts.

According to co-creator Gregg Mayles, the idea behind "Stop 'n' Swop" was to do certain challenges/objectives in Banjo-Tooie, then stop and swap the cartridges while the system was still on. This would have unlocked special items in Banjo-Kazooie. You can than swap the games again to get the items in Banjo-Tooie, and this would potentially extend to future Rare games, including Donkey Kong 64. This idea was scrapped when the window of time that players could "hot swap" games (the ability to switch games when the power was on) was shortened from 10 seconds to only 1 second. There are still cheat codes that will unlock the special items in Banjo-Kazooie. In the Xbox Live Arcade versions of both games, the methods to obtain the Stop 'n' Swop items were changed to instead be tied to recognizing save data for Banjo-Tooie or Banjo-Kazooie: Nuts & Bolts. In the 2026 Evercade ports of the games, the Stop 'n' Swop system is reimplemented after beating the game, and allows players to unlock additional cheats, and a music player featuring early unused versions of certain level themes.

Inside the Dodgems Dome in Witchyworld, looking out of the window you can see a constellation of Rare's then mascot, Mr. Pants. He also makes an appearance on a TV in Hailfire Peaks, inside Boggy the polar bear's igloo.

Donkey Kong makes a cameo in the original Nintendo 64 version of Banjo-Tooie in the form of a plush doll held by one of Bottles' children, Goggles, obviously referencing how Rare developed games for both franchises at the time. While this doll would reappear in the game's Xbox Live Arcade remaster in 2009, its texture was modified, with DK's brow ridge replaced by generic googly eyes to avoid any potential legal issues with Nintendo. The original texture and doll design would later be restored for Banjo-Tooie's re-release on Nintendo Switch Online in 2024. For the 2026 Evercade port of the game, this doll would instead be replaced with one of Conker.