ZenGems is a standard color-matching game where the player has to make combinations of three or more spheres of the same color. The game screen is a grid with a mouse-controlled ball shooter at the top that moves horizontally.
The game has three modes: Arcade, adventure and strategy. In the arcade mode the bottom half of the grid is underwater. The goal is to eliminate all the balls, obstacles and jewels that are over the water line.
Adventure mode is the only one with a storyline. A boy called Hoshiko must retrieve the medallions of virtue, stolen from the temples and hid inside puzzles by magician thieves. After solving the puzzle by eliminating all the spheres from the grid, a gold piece is put in its place, slowly rebuilding a complete medallion.
Strategy mode has no set goal, it is a resistance mode where the player can choose any of the worlds of adventure mode as the starting point and play until it is impossible to keep up with the game pace.
Besides the colored spheres, the grid is filled with other objects and power-ups. Jewels break when falling down two spaces or more, and crack when falling down one. Some balls are encased in boxes and immobile, they need to be matched to be released. Stones can only be broke with the fireball power-up. The fireball destroys three pieces in a row, but is ineffective against jewels. A ball with a curved arrow pushes a line of spheres before resting in its place. ColorBursts, jars with colored liquid, change the surrounding balls to its own color. Energy balls clear from a column all the spheres and boxes that have its color.
The grid is constantly refilled with balls. If they reach the top, the game is over.