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.

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.

Tiptup is a recurring NPC character in the Banjo-Kazooie series that, along with Banjo, also made his debut in Diddy Kong Racing in 1997. However, Tiptup was originally the name of a turtle in Dream: Land of Giants, the game that would eventually morph into Banjo-Kazooie. Halfway through the development of BK, the development team behind Diddy Kong Racing (or Pro-Am 64 as it was called before Diddy Kong was included later on) were in need of names for their racers, one of which happened to be a turtle, and thus it was given the Tiptup name. Tiptup was then incorporated into future Rare games like Banjo-Kazooie and Banjo-Tooie.

Cauldron Keep, the last "level" in Banjo-Tooie, was originally intended to be a fully-fledged final world with its own extra set of 10 Jiggies and challenges to complete. According to series head Gregg Mayles, it ended up being massively cut down in scope due to time constraints, now only featuring a third battle against Klungo, the Tower of Tragedy Quiz and the final battle against Gruntilda in the HAG-1 at the top of the tower. This would also explain why Banjo-Tooie only features 90 Jiggies, in comparison to its predecessor that featured 100.

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, and this change was not applied to the Xbox Live Arcade 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.

The Breegull Bash move in the Japanese versions of Banjo-Tooie and as well as Super Smash Bros. Ultimate is called ハリセンカズーイ(Harisen Kazui), which literally translated into English is "Slapping Fan Kazooie". A harisen is a giant paper fan that is typically used as part of a manzai act, where the straight man smacks the funny man in response to their jokes or foolishness. The "Fan" item that appeared in Super Smash Bros., Super Smash Bros. Melee, and Super Smash Bros. Brawl is actually a harisen, and it's even called as such (はりせん) in the Japanese version of those games as well.

It's worth pointing out that in general, the Japanese localizations for the Banjo-Kazooie games seem to exclude any mention of the word "Breegull", the name of Kazooie's species. This is something Masahiro Sakurai made note of when showcasing Banjo & Kazooie's moveset in Super Smash Bros. Ultimate.

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.

In the Japanese version of Super Smash Bros. Ultimate, Banjo & Kazooie's down special, Rear Egg, is called おケツタマゴ (Oketsu Tamago), which in English directly translates to "Ass Egg". This particular name was utilized for the Japanese localization of Banjo-Kazooie, at least its Japanese website.

It's worth pointing out that, in the English version of Banjo-Kazooie and Banjo-Tooie, this move has no name, as it's rolled into Egg Firing as one ability. However, internally in both games, the animation is indeed named "egg ass", which the Japanese version literally translates for its name.

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.

Banjo-Tooie has become somewhat infamous for its large-scaled and convoluted structure in comparison to its predecessor, Banjo-Kazooie, with far more larger interconnected worlds with longer, complex puzzles that typically require backtracking, in comparison to Banjo-Kazooie's more straightforward and compact, self-contained levels and objectives.

According to Steve Malpass, one of Banjo-Tooie's game designers, the game was designed more in the vein of an adventure game as opposed to a platformer, being heavily inspired by The Legend of Zelda: Ocarina of Time in particular. The development team was aware of how overcomplicated the game's structure had become by its launch (the QA department was vocal about the backtracking and navigation issues), but it was ultimately too late for them to streamline it. The Warp Pads found throughout the worlds were actually included after the levels were designed, as an attempt to mitigate the aforementioned navigation issues.

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.

One of the characters planned for Dream: Land of Giants before it was morphed into Banjo-Kazooie was Captain Cockeye, a friendly pirate character that was also described as being "a bit of a mad professor".

While this character wouldn't appear in the final Banjo-Kazooie game, Banjo-Tooie's character Pawno seen in Jolly Roger's Lagoon serves as a homage to him, by wearing his clothing as noted by former Rare character designer Ed Bryan.

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.