Metroid Zero Mission was a triumphant retelling of the original Metroid story, and the music was given a substantial update as well. Kenji Yamamoto and Minako Hamano consulted with Metroid composer Hirokazu Tanaka to ensure the music was true to the original. Most tracks have been extended, such as "Kraid's Lair", which adds an impressive choral section, though its change was not the most dramatic. "Norfair" received one of the biggest improvements, with a lilting flute and bubbling choir. "Ridley's Lair" also received a major overhaul, dumping the intensity of the original in favor of a slower and creepier ghost-filled corridor. Finally, there are two versions of "Brinstar".

Yamamoto-san also tied the series together aurally by integrating Metroid Primestyle Chozo themes, as well as a nice reference to the Super Metroid "Title" theme in the "Metroids Appear" cutscene. There are also remixes of "VS. Ridley", "VS. Kraid", "Spore Spawn", and "Space Pirates Appear", as well as two clever arrangements of "Wrecked Ship" from Super: the low and menacing "Crateria" and the jazzy, sneaky "Space Pirate Mother Ship".

However, the instrument selection is somewhat inferior to that of Fusion, owing to the different art style and the legacy of the original themes. Still, the soundtrack manages some fantastic bass, particularly "VS. Mecha Ridley" and the Japanese version of the "Escape Theme", and it also has excellent choral synths, such as those found in the "Ending" theme, and a nice organ with "VS. God of War". Overall, an excellent score and fantastic homage to the original. This soundtrack was created with VBA-M r956, with a -0.3 filter to closely emulate the actual GBA sound hardware.