Alien Bubbles is a bubble-shooting arcade game that mimics elements from the classic Puzzle Bobble (Bust-a-Move) game. The player must stop floating, round alien heads from touching a dinosaur near the shooter or the bottom of the playfield. If the aliens reach the bottom of the screen, they explode and take everything nearby with them. If they come into contact with the dinosaur, they turn it into ash.
The player's goals are to clear the screen of all aliens and earn points. The game features a gear shooter with a center projectile area designed for a large arrow. The player directs a colored arrow at a bubble with a matching color. Unlike some shooters, the player doesn't need to perform a connect-line or match-3 maneuver. They only need to shoot single heads with the shooter's basic colored arrows. That said, they must shoot with precision. The game speeds up the drop of an alien if the player hits the head with an arrow of a different color.
Alien Bubbles offers the player levels and infinite play. It also offers fast-play options. The player can use a white, rainbow-colored, crystal arrow powerup to pierce through a large swath of non-matched heads. They can also use an explosive-tipped arrow powerup to blow up several non-matched heads.
After they remove all alien heads, the game supplies them with new backgrounds and challenges.