Maya Bubbles is a bubble shooter. Across three scroll-style maps that feature 120 levels, the player explores various locations associated with the Mayan culture by completing bubble-popping tasks. They use a mask-style shooter and projectiles to remove bubbles attached to floating locked boxes. Their goal is to collect a key in each level that unlocks the next one and earn the highest possible score per level.
The player pops bubbles by matching the color and pattern of a projectile with a cluster of two or more linked bubbles. If the primary projectile doesn't match a nearby cluster, they can swap it with the secondary one in the mask's mouth. Their goal is to create groups that contain three or more matching bubbles. When the bubbles pop, each one releases energy. When the lock box eventually unlocks, the key automatically opens the next spot on the map.
Maya Bubbles tries to make the player miss shots by having animals move or run around in the background. Although the game doesn't feature a penalty countdown clock, it only allows the player to use a specific number of moves per level. They can review this number at any time in the lower-left area.