La banda sonora de Prototype fue compuesta por Cris Velasco y Sascha Dikiciyan.
Tracklist[]
1. Alex Theme (02:13)
2. Memory in Death (02:36)
3. Things to Come (02:02)
4. In the Web (02:07)
5. First and Last Things (02:22)
6. Alex Awakes (02:14)
7. A Dream of Armageddon (03:08)
8. The Stolen Body (01:50)
9. A New Order (02:24)
10. Main Menu (02:38)
11. Under the Knife (02:30)
12. On Instinct (02:00)
13. Behind the Glass (02:02)
14. Errand Boy (02:45)
15. The Wheels of Chance (01:29)
16. Open Conspiracy (02:41)
17. Men Like Gods (02:10)
18. Biological Imperative (01:53)
19. Past and Present (02:08)
20. The Door in the Wall (02:05)
21. The Last Man (02:39)