An unreleased soundtrack will soon be available featuring all the unreleased tracks from the game. (More Info)
| # | Title | Artist |
| 1. | in the beginning, there was.... | Deb Lyons |
| 2. | first meeting | Deb Lyons |
| 3. | Xenosaga Ⅱ opening theme | Yuki Kajiura |
| 4. | assault | Deb Lyons |
| 5. | strain～Jin | Deb Lyons |
| 6. | here he comes | Yuki Kajiura |
| 7. | fatal fight (Jin & Margulis) | Deb Lyons, Tokyo Philharmonic Chorus |
| 8. | R&D report | Yuki Kajiura |
| 9. | chase | Yuki Kajiura |
| 10. | surrounded | Yuki Kajiura |
| 11. | lamentation | Yuki Kajiura |
| 12. | Albedo | Yuki Kajiura |
| 13. | communication breakdown | Tokyo Philharmonic Chorus |
| 14. | Sakura (theme-piano ver.) | Yuki Kajiura |
| 15. | Sakura #2 (theme-simple voc.ver.) | Margaret Dorn |
| 16. | strained | Yuki Kajiura |
| 17. | Jr. #2 | Yuriko Kaida |
| 18. | strained #2～Albedo #2 | Yuki Kajiura |
| 19. | in the beginning, there was....#2 | Deb Lyons |
| 20. | battle of Elsa | Yuki Kajiura |
| 21. | here she comes (KOS-MOS) | Yuki Kajiura |
| 22. | battle of Elsa #2 | Yuki Kajiura |
| 23. | gate out | Yuki Kajiura |
| # | Title | Artist |
| 1. | here he comes #2 | Deb Lyons |
| 2. | creeping fear | Yuki Kajiura |
| 3. | U-DO～Febronia | Yuki Kajiura |
| 4. | final crisis | Yuki Kajiura |
| 5. | presentiment～Jr. #3 | Yuki Kajiura |
| 6. | a field of battle～bitter #2 | Yuriko Kaida |
| 7. | inside～Sakura #3 | Yuriko Kaida |
| 8. | I am free | Yuki Kajiura |
| 9. | Sakura #4 (theme-gentle strings ver.) | Yuki Kajiura |
| 10. | Sweet Song (Xenosaga Ⅱ ending theme) | Margaret Dorn, Tokyo Philharmonic Chorus |
| 11. | Jr. | Margaret Dorn |
| 12. | Jr.#4 | Yuki Kajiura |
| 13. | fatal fight #2 | Deb Lyons, Tokyo Philharmonic Chorus |
| 14. | bitter | Yuriko Kaida |
| 15. | Nephilim | Yuki Kajiura |
| 16. | the image theme of Xenosaga Ⅱ #piano ver. | Deb Lyons |
| 17. | the image theme of Xenosaga Ⅱ | Deb Lyons, Tokyo Philharmonic Chorus |
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