On the third file select, you can see Banjo and Kazooie playing a Game Boy. The sound effects coming from the Game Boy are from Donkey Kong Land. Oddly enough this would still be featured in the Xbox Live Arcade version. In the 2026 Evercade version however, the Game Boy would be replaced with Evercade's Rare-themed Super Pocket handheld console.

In the original Nintendo 64 version, if you input too many "illegal" cheats in the sandcastle in Treasure Trove Cove, Gruntilda will permanently delete your save file. This won't come into effect until you have saved and quit or turned off the console though.

In the Xbox Live Arcade version, entering any cheat except for those given by Cheato and Bottles will disable saving for the current playthrough and remove the player's score from the leaderboard. Oddly enough, there is no penalty for inputting too many cheat codes in this version, even though all the text about erasing the save file is retained. This was fixed in the 2026 Evercade port of the game.

A poster featuring an early design of Berri from Conker's Twelve Tales can be found in Rusty Bucket Bay. This would be replaced by a poster of Conker as he appears in the reworked version of that game, Conker's Bad Fur Day, in the Xbox Live Arcade version.

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.