On the bottom floor of Boggy the polar bear's igloo in Hailfire Peaks, on two of the kid's beds are the Perfect Dark logo and Banjo-Kazooie promotional artwork.

In Jolly Roger's Lagoon, there is a pig named Chris P. Bacon who is trying to take underwater pictures of the ruins. Looking closely at the camera he's using reveals that it's actually a Game Boy Color with a Game Boy Camera attached. This is retained in the Xbox Live Arcade version of the game despite it being on a console from a rivaling company.

In Jolly Roger's Lagoon is a sunken space ship near the Atlantis Area. Upon entering the UFO, Banjo and Kazooie meet four aliens, and Kazooie asks "Are any of you called Elvis?" This is a reference to another Rareware Game, Perfect Dark, in which there is an an alien named Elvis. This in turn refers to a number of theories that the entertainer Elvis Presley was an alien.

In 'the Workers Quarters' of Grunty's Industries, you can find Loggo in the men's bathroom, who has something clogged inside him. If you talk to him for a second time before unclogging him, Kazooie will bring up the option of calling a plumber and mentions 'Mario' by name. In the Xbox Live Arcade version, the reference is changed to "that well known Italian guy" as Microsoft could not use Mario's name.

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.

Inside the giant trash can in Cloud Cuckooland, You can find a giant milk carton with Tooty's face on it which reads "Missing. Last seen in Banjo Kazooie." This is a joke that references the fact that she does not appear anywhere in the game.

In Banjo-Tooie at Jolly Roger's Tavern, you can find a man by the name of Captain Blackeye. He repeatedly states "Once, I had a dream..." and tells of a bear who stole his glory. This is a reference to Project Dream, the first version of Banjo-Kazooie. He was meant to be the main antagonist of the game.

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.