WarioWare's core gameplay principles revolve around the concept of "microgames", minigames that must be completed within a demanding time limit. In a stage, microgames are presented to the player consecutively, and as the player keeps playing, the game speeds up, making microgames' time limits shorter and forcing the player to complete them faster. If the player completes a microgame, the game moves onto the next one, while if the player fails a microgame, by either losing the game or running out of time, one of four lives will be deducted. If the player loses all four of their lives, the game will end and the player's score (the number of microgames played) will be saved if it is one of their best three scores.

At the end of a set number of microgames, the player must complete a "boss stage"; a longer microgame without a set time limit. In these microgames, the player has the opportunity to gain an extra life, but only if the player has less than four lives. Mega Microgames! has nine stages, each revolving around Wario or one of his associates in a plot scenario. Each stage also has a general theme the microgames present in it pertain to, such as "Sports" or "Nintendo Classics". In addition to microgames, the player is also able to gain access to additional bonus minigames to play.

Mega Microgames! contains 213 microgames, split over 9 stages, each with different themes and following the story of different characters, all associates of Wario whom are contacted by him to make games for him to sell as part of his new "game" company. The game's story is conveyed through short subtitled cutscenes before and after stages. In addition to microgame stages, the player can unlock "remix" stages which feature microgames from past stages in it, as well as other bonus stages, which feature all microgames, but change elements like speed or microgame difficulty.

The player is also able to gain access to other bonus minigames if they beat or get a high score in certain main stages. The minigames are typically variations on concepts of existing microgames from main stages, and take the form of both single-player games and multiplayer games.