The legendary seven Rainbow Bells have been stolen by the evil scientist Dr. Warumon, who plans to use them to conquer the world, and Princess Melora, the symbol of people's hope, has disappeared. Dr. Cinnamon's three fighters, TwinBee, WinBee and GwinBee, are sent to get the Rainbow Bells back and stop Dr. Warumon's ambitions.
As opposed to the standard scrolling shoot-em-up gameplay featured in most TwinBee games, Rainbow Bell Adventures is a typical side-scrolling platformer, similar in concept to that of Rocket Knight Adventures, in which either TwinBee, WinBee or GwinBee must get to the end of a stage.
All characters use their punch to attack, which can be charged to unleash a punch wave. They have two sets of weapons, one of them is either a short or long-ranged weapon (a hammer for TwinBee, a ribbon for WinBee, and throwing rattles for GwinBee), and the other one is a gun, which is a reference to a cutscene from Detana!! TwinBee in which TwinBee is shown with two guns on each hand. All three can temporally fly in eight directions by propelling via a rocket pack that must be charged, as well as hover.