The puzzles of Vermithrax II involve swapping gems into unoccupied spaces of the game board to create matches. A brief tutorial regarding this technique is given upon reaching the planet for the first time. All the puzzles are arranged in various formations and patterns.
Completing any four of Vermithrax II's five puzzles unlocks access to Maya III, the next planet in Puzzle mode.
- The mechanic of swapping gems into empty spaces of the game board was later used in Bejeweled 3, specifically in the Avalanche mini-quests of Quest mode.