Metroid Prime Pinball did a fantastic job of taking Metroid Prime's high-quality soundtrack and shrinking it down to the DS. With the exception of the wrecked ship theme, all the best tracks from Prime are here, along with "Hunters" from Echoes in the form of the "Multiball" theme, itself an arrange of the green Brinstar theme from Super. However, most of the tracks have been shortened due to the smaller storage capacity of a DS cartridge, but enough of the main melody remains to provide an enjoyable listen. In the case of "VS. Thardus", additional material has also been added, perhaps unused ideas.

The arrangements get the most out of the DS sound chip to make up for , such as "Space Pirate Panic", which makes excellent use of dynamic drum synths, and "Battle Theme 2", which has some great metallic percussion. However, arranges of tracks such as "Magmoor" and "Phendrana Drifts" illustrate the limitations of the DS all too well, coming out in heavily buzzing MIDI rumbles or airy, wavering wisps. However, Kenji Yamamoto and Masaru Tajima also made use of streamed audio with "Phazon Mines ~ Impact Crater", "VS. Omega Pirate", and the amazing "Space Pirate Frigate" theme, which is a full-blown rock arrange of "Brinstar" from the original Metroid and by far the best track in the game. It was later arranged for Super Smash Bros. Brawl. The recorded audio sounds fantastic on the DS, especially the guitars in "Space Pirate Frigate".