The game has pre-set stages surrounding a central hub. In addition, every 10 stages concludes the current hub with a boss battle. The game consists of 80 stages; 40 standard levels and 40 hidden challenge levels unlocked by collecting three chests hidden within a standard level. The 40 standard levels provide an average of ten hours of gameplay. The protagonist has access to an unlimited amount of jelly beans, although the type availability is pre-set at the beginning of each level. Completing challenge levels unlocks bonus developer material such as concept art and story boards."...to journey deeper into most stages, you must tap the Z button, which cues the jelly bean wheel. Here, you'll find a wide assortment of beans that, when fed to the [blob], induce his changes into convenient tools. A ladder for climbing; an anvil for dropping on enemies' heads; a cannon for shooting the boy to otherwise unattainable areas; a spaceship for flying around stages; a crank for lifting platforms and obstructions; a bouncy ball for floating across waters; a trampoline for springing into the air; and even a hole so that the boy can fall through platforms to walkways below."
A Boy and His Blob does not utilize the Wii Remote's motion detection or IR controls, and is controlled either by the Wii Remote (with the Nunchuk accessory) or by the Wii Classic Controller. Many reviewers have noted the "hug" button, which serves no in-game purpose except to hug the blob companion.