After the game was originally released, a director's cut was released in Japan. This version included optional dungeons, Veronica Vera and Lenny Curtis as playable characters, extra scenes, and new items. It also had a slightly bigger Judgment Ring, and supported the PlayStation 2 Hard Drive attachment.

The good ending Spoiler:sends the main characters Yuri and Karin through time to separate locations. Yuri will travel to the beginning of the first Shadow Hearts game, and Karin will travel further back in time, revealing that she will become Yuri's mother.

Solving the Book of Solomon and finishing all of King Solomon's Trials (Pit Fights) unlocks an optional boss battle with King Solomon himself. Defeating him unlocks the game's most powerful spell, Melt.