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.

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.

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.

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.

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.