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.

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.

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.

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.

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.

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.

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 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.

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.

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.

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.

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.

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.

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.