| # | Title | Rating | Length |
|---|
| 1 | System Jingle | | 0:09 |
| 2 | Metroid Prime 3 Title Music | | 3:03 |
| 3 | Dark Samus | | 1:22 |
| 4 | In The Cockpit | | 2:06 |
| 5 | GFS Olympus | | 4:25 |
| 6 | Save Station | | 1:18 |
| 7 | Aurora Chamber | | 3:52 |
| 8 | Galactic Federation Battle Theme | | 2:15 |
| 9 | VS. Space Pirates | | 1:53 |
| 10 | VS. Crawltanks, Hunter Metroid | | 3:12 |
| 11 | Tension | | 7:11 |
| 12 | VS. Berzerker Lord | | 3:26 |
| 13 | Landing on Norion | | 0:23 |
| 14 | Norion | | 5:42 |
| 15 | Rundas | | 2:01 |
| 16 | Generator Room | | 2:04 |
| 17 | Crisis | | 2:51 |
| 18 | Gandrayda Defeats the Space Pirates | | 0:20 |
| 19 | VS. Ridley | | 2:12 |
| 20 | Dark Samus Returns | | 1:04 |
| 21 | Galactic Federation Theme (Theme of Super Metroid) | | 3:27 |
| 22 | Bryyo | | 14:52 |
| 23 | VS. Reptilicus | | 0:48 |
| 24 | Bryyo Fire | | 6:51 |
| 25 | Phazon Area | | 0:57 |
| 26 | The Corruption | | 5:00 |
| 27 | VS. Large Space Pirate Force | | 1:09 |
| 28 | VS. Rundas | | 6:11 |
| 29 | Bryyo Thorn Jungle | | 4:55 |
| 30 | Phazon Seed | | 3:28 |
| 31 | VS. Mogenar | | 4:33 |
| 32 | Phazon Seed Destroyed | | 0:12 |
| 33 | Outer Space | | 0:37 |
| 34 | SkyTown | | 7:07 |
| 35 | Item Room | | 1:47 |
| 36 | VS. Steamlord | | 0:56 |
| 37 | VS. Defense Drone | | 1:16 |
| 38 | VS. Ghor | | 2:54 |
| 39 | Bryyo Ice | | 7:15 |
| 40 | Xenoresearch | | 4:57 |
| 41 | VS. Helios | | 2:57 |
| 42 | Environment Sound (Disquieting) | | 3:51 |
| 43 | VS. Metroids | | 1:39 |
| 44 | VS. Gandrayda | | 4:33 |
| 45 | Pirate Homeworld | | 5:26 |
| 46 | GFS Valhalla | | 3:55 |
| 47 | GFS Valhalla Depths | | 5:40 |
| 48 | Admiral Dane (Galactic Federation Theme Reprise) | | 2:52 |
| 49 | VS. Omega Ridley | | 3:44 |
| 50 | Phaaze | | 3:12 |
| 51 | VS. Dark Samus | | 3:46 |
| 52 | VS. Aurora Unit 313 (Body) | | 3:26 |
| 53 | VS. Aurora Unit 313 (Head) | | 1:16 |
| 54 | Ending Part 1 - Last Stand | | 2:17 |
| 55 | Ending Part 2 - Memoriam | | 1:12 |
| 56 | Ending Staff Roll | | 4:33 |
| 57 | Record of Samus | | 2:50 |
| 58 | Epilogue | | 0:54 |
| 59 | Samus Appearance Jingle | | 0:10 |
| 60 | Event Jingle | | 0:04 |
| 61 | Item Obtainment Jingle | | 0:08 |
| 62 | Tank Obtainment Jingle | | 0:05 |
