Magical Bubble Shooter is a bubble-popping game with a magical creature and a space theme. On a nighttime planet in view of other worlds, the player pops groups of three or more bubble balls with matching projectiles to rescue baby magical creatures trapped in some clusters, earn high points, and clear the playfields. To earn the highest score possible, they must complete this task quickly and without using a lot of the available projectiles. They must also attempt to earn three stars per level to prove their bubble-shooting skills.
The game features 24 levels. Unlike many similar games, the player doesn't have to win a level to unlock another one. They can select any of the levels to play at any time. They receive a dotted aiming line to help target specific areas. The game also allows the player to swap bubbles using a button marked with two semicircular arrows against a rock near the creature to make repeated combination hits possible. The player shoots bubble projectiles floating above a magical creature's head on each level. They can shoot targets in a straight line or angle shots off the sides of the playfield.
Magical Bubble Shooter provides the player with a vertical progress tracking bar in the upper-left corner that turns gradient orange as it fills. They can track the number of remaining projectiles on a wooden sign at the lower-right corner. That said, the game also features a distraction element. Each creature's mouth opens and closes during play.