In the Japanese release, Trotty, the pig who grew a third arm from being pushed into the contaminated pool in Jolly Roger's Lagoon, is altered to remove references to his deformity. Not only is the third arm edited out of his model, but his dialogue is also rewritten; instead of worrying about growing additional limbs, his concern is that the polluted water will damage his swim trunks and beach ball. In the Japanese version of the Xbox Live Arcade port, Trotty's third arm is restored, but his dialogue remains censored.

In the ending cutscene in the Japanese version, Gruntilda's skull was replaced with a sack that resembles her clothing. This change was most likely made to comply with political outcry in Japan over the 1997 Kobe child murders, during which a 14 year-old boy murdered two fellow students on separate occasions, the first victim having been beheaded. The cryptic nature of these crimes garnered enough attention in Japanese media and politics to cause the National Diet to reduce the age of criminal responsibility in Japan from 16 to 14 years old in the year 2000, the same year Banjo-Tooie was released. Despite this change, Gruntilda's eyeball can still be seen falling out of the bag in the censored version.

In Grunty Industries, there is a small chance that when going to the Worker Quarters, the player can spot light emanating out of a restroom where a worker rabbit can be heard taking a rather huge "dump".

The combination code to obtain the Jiggy belonging to Superstash the Safe in Cloud Cuckooland's central cave is 1984, which the safe describes as "a Rare Date". This is a reference to the year that Rare was founded, 1984.

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.

One of the main characters in the game is the military brother of Bottles, Jamjars. This name was actually first used in Banjo-Kazooie during the opening training. As the player is testing out Kazooie's beak barge, Bottles comments that Kazooie is useful for something, to which she retaliates with, "I'm trying this move out on you next, jam jars!" The term comes from slang for large glasses with thick lenses.

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.

It's possible to slow down the Star Spinner in the Space Zone section of Witchyworld by launching a Grenade Egg at the control panel to the left of the entrance.

Sabreman can be found on the ice side of Hailfire Peaks. Sabreman is a an old character from the Sabreman series, developed by Rare under their original name of "Ultimate Play the Game". Sabreman references his old games when the player unfreezes him, saying that he has been trapped in there since 1984, the release year of his first game Sabre Wulf.

Once the player takes Sabreman back to his tent on the fire side of Hailfire Peaks, he will begin to ramble about perhaps riding a dolphin. This may refer to the code name for the GameCube. If Rare had not been bought out by Microsoft, it is possible that the Sabreman series reboot, Sabre Wulf, would have been made for the GameCube rather than the Game Boy Advance.

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.

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.

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 XBLA version, the reference is changed to "that well known Italian guy" as Microsoft could not use Mario's name.

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.

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.