In flashback scenes in the game, Adam Malkovich commands the Galactic Federation Battleship VIXIV. This battleship is named after the starship "Space Tank VIXIV" from the 1992 Japan-only Game Boy game X, which was also directed by Metroid: Other M's director and producer Yoshio Sakamoto.

In Metroid: Other M, Samus Aran has a mole under the left side of her lip. This was the first Metroid game to add this detail. However, it had been mentioned before. Co-creator of the Series, Yoshio Sakamoto, stated in an interview after the release of Super Metroid that he was the only person that knew of the location of Samus' beauty spot. A mole was also drawn on Samus' face in concept art for Metroid Prime, but did not appear in the game.

Metroid: Other M confirms that the original Ridley, Spoiler:despite all of his previous defeats, had always survived each encounter. It is only in Super Metroid where he is killed for the first time.

Multiple test rooms can be found in the games data. One of these is actually the 1st boss arena from Ninja Gaiden 2, where the player fights Rasetsu. The background tower is no longer part of the model, but the structure is mostly intact.

The Head Quarantine Officer instructing Samus through her training sequence during the beginning is voice acted in English by Nate Bihldorf. Bihldorf localized Metroid: Zero Mission and contributed to Metroid Prime 2: Echoes and Metroid Prime 3: Corruption. In an interview with ShineSparkers, he explained his experience: "I thought I sounded like a nerd - but that's what Mr. Sakamoto was looking for, so I guess I'd call it a resounding success." The Quarantine Officer has an uncanny visual resemblance to Dan Owsen, who narrated the opening line of Super Metroid: "The last Metroid is in captivity. The Galaxy is at Peace...".

In the Subspace Emissary mode in Super Smash Bros. Brawl, there is a cutscene where Ridley grabs Samus and drags her along the wall. He only lets go when Pikachu zaps him with a thunder bolt. This cutscene seems to have influenced a similar scene in Metroid: Other M, where Ridley does the same, only to be shot by Anthony.