This game remixes several songs from Yu-Gi-Oh! Forbidden Memories as well as using original songs, so it's going to have a good soundtrack.
- Seto's arrival theme is amazing, and well worth playing through the story again to hear.
- Seto's battle theme gets a remix. It's spectacular and classical in its rhythm and gives the impression of fighting an Anti-Hero who's not about to stop his goals.
- Yugi's theme sounds just wondrous and mystical with a hint of desperation since you're about to beat the Big Good and turn the tide of a war against him.
- The Yorkist battle theme is awesome and upbeat, perfect for battle against the weaker members of the Rose Crusaders.
- The Lancastrian battle theme is elegant and classical, which makes this Soundtrack Dissonance since you're fighting to it.
- The Custom Duel theme gives a more serious remix of the tournament theme from the previous game. Bit of a waste since you'll never hear it anywhere outside the game's two-player mode against the various deck masters.
- Manawyddan fab Llyr has two themes depending on whose side you're on when you fight him, one for the Yorkist side and one for the Lancastrian side. The former remixes the ever-intimidating High Mage duels, and the latter remixes the dangerous Final Boss.