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.

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 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 '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.

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.