Banjo-Kazooie started development on the SNES and was titled "Project Dream" or "Dream: Land of Giants". The game was going to be an RPG, and the main character would have been a young man named Edison who had caused trouble with a group of pirates led by a man named Captain Blackeye.

On the title screen, there is a slight chance that you may get an alternate file select animation. These include Banjo being flipped out of his bed and out his window, the wall in Banjo's kitchen spinning around, and Banjo being launched out of his chair.

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.

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.

Napper the Ghost and Clanker's voices are both Banjo's voice but slowed down and lowered respectively. This was done due to not enough memory space on the cartridge to add additional voices.

The music played inside the Ant Hill of Mumbo's Mountain is a slowed down version of what was originally intended to be the world's main theme. The original theme was partially inspired by the Baby Elephant Walk tune from the film "Hatari!".

The theme that was used for the world Treasure Trove Cove was also the second version that the game's composer, Grant Kirkhope, had written due to the change of the game from "Project Dream" to "Banjo-Kazooie".

When Mumbo turns you into a creature he says "Oominaka." Grant Kirkhope, Mumbo's voice actor, revealed that at the time of recording the voices for the game his left testicle was swollen. "Knackers" is British slang for testicles, so he thought it would be funny if Mumbo said "Ooh, my Knackers." Thus, every time that Mumbo uses his magic to turn you into a creature, he's actually complaining that his testicles are in pain.

When you collect a Mumbo Token, a sound effect of Mumbo saying "Ikkum Bokum" plays. This phrase (and most of Mumbo's speech aside from "Oominaka" and a few other sound effects) are all made up of randomly-arranged soundbites. When these soundbites are arranged in the correct order, they say "Come and have a go, if you think you're hard enough."

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.

There's an unused firefly sprite which appears similar to the Beehive's Bee sprite which even uses the same wings. It's possible this was intended to be used for the world Mad Monster Mansion, the only level set during night.

Grant Kirkhope, the composer of the game, provided the voice of the pots in Mad Monster Mansion that say "Thank You" when the player deposits an egg in them. According to Kirkhope, he had to redo the line several times because Nintendo thought he was saying "Fuck You".

An image of Donkey Kong appeared in an early build, but was replaced with an image of Banjo's sister, Tooty.

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.

In an early E3 video, it shows that Banjo and Kazooie could fly at any time they wanted without the use of a flight pad. This was most likely removed to limit the amount of area the player could cover at one time.

Inside Banjo's house is a portrait of Banjo & Kazooie walking through a forest. While commonly believed to be an early screenshot of the level Fungi Forest which would later appear in Donkey Kong 64, this is actually a screenshot from an early build of Banjo-Kazooie's prototype Dream: Land of Giants, after the original protagonist was replaced by Banjo.

The music for Gruntilda's Lair strongly resembles an old song called "Teddy Bear's Picnic". The composer, Grant Kirkhope, has acknowledged that he probably was thinking of Teddy Bear's Picnic when he wrote Gruntilda's Lair, but doesn't remember it being a conscious decision.

There is a unused test map in the game's data. It consists of 8 slopes arranged in a circle formation. This test map was most likely made to test Banjo's climbing ability.

The original sound for collecting an Egg changed in development. It's not know why it was scrapped, but it might have been because the sound became rather annoying when collecting large amounts of eggs.

Inside the game's data is an unused sign that says "On Vacation" It was most likely originally intended to be used for Mumbo's hut in the Winter area of Click Clock Wood. Instead, a Beehive tells Banjo that Mumbo is on vacation.

In an early development version of Mad Monster Mansion, there was a painting in the dining room of the windmill from Twelve Tales: Conker 64 - The game that would later become Conker's Bad Fur Day.