The planet where Alph, Britanny, and Charlie come from is called "Koppai." This is a reference to Nintendo's origins, as the company was founded in 1889 as "Nintendo Koppai".

When the game's characters were just starting to be released, there were to be 4 playable characters, A (Which became Alph), B (Which became Brittany), C (Which became Charlie), and D. Nobody currently knows what happened to character D, but it's speculated that because the crew's ship is named the Drake, many aspects of Character D were given to the ship.

Nintendo experimented with the possibility of putting Pikmin 3 on a handheld system like the DS and 3DS, but the gameplay boiled down to micro-management on the touch screen and didn't feel like a Pikmin game.

Even though the naming nomenclature fits in with NASA's methods of identifying unimportant planets, the Pikmin planet "PNF-404" is potentially also a pun; "404" is a HTML status code for "Page Not Found", or "PNF".

During development of Pikmin 3, a screenshot was shown of Brittany wearing a yellow suit instead of the pink suit she wears in the final release.

In the Japanese version of Pikmin 3, the Scaly Custard (avocado) is literally translated as "Crocodile Scrotum" (ワニノフグリ).

If the player has a group containing 20 of each Pikmin type they will sing the theme song for the game.

The Bearded Amprat is the only enemy in the series to have a visible anus.

An unused enemy named "iwadama" was found in the game files. The creature shares many characteristics with the Beady Long Legs from Pikmin and Pikmin 2. However, instead of the spherical head the boss normally has, it is replaced with a large foot of the boss, possibly implying it would stomp it's head into the ground as well, and may have been a reimagining of the boss. It's unknown why it was cut, but it's possible it was replaced with the Shaggy and Baldy Long Legs in the final game.