The gameplay in Wario Land 3 is very similar to that of its predecessor, Wario Land II. Wario must take advantage of his enemies' attacks to physically change and access new areas. For example, if Wario eats a donut thrown by a certain enemy, he temporarily bulks up to twice his size, giving him extra protection against attacks and the ability to break certain blocks. While Wario will always be affected by his enemies, he must also find new powers and abilities in order to progress through the game.
The world of the music box is divided into four different areas, East, West, North, and South, with a total of 25 individual stages spread between them.[4] Each stage contains four treasures, for a total of 100, each of which is locked in a colored treasure chest that can only be opened with the corresponding key. The colors of the chests are, in the approximate order that they are intended to be opened, Gray, Red, Green, and Blue. This order is not fixed, although the game provides hints as to the next stage to travel to and the next treasure to obtain. Often, when a treasure chest in one stage cannot be reached, Wario must backtrack to retrieve a new item to make it accessible.[5]
Finding new treasures usually opens a path to a new stage, or unlocks a new area in a previous stage. Some treasures grant Wario a new ability, allowing him to access previously unreachable areas. Whenever Wario obtains a new treasure, he is transported back to the music box overworld. Time alternates between day or night each time Wario exits a stage. Some stages change depending on the time of day; certain enemies may be replaced or different paths may open up.[6] Wario cannot control time initially, but gains this ability when he finds a certain treasure.[7]
In some stages, Wario will have to play a golfing minigame to progress.[8] He must knock the enemy into the cup without going over par for that hole, while avoiding hazards such as water, bunkers, lava and rough. Upon collecting certain treasures in the game, this golf minigame is available to be played at any time from the overworld map.[7]