On his treasure-seeking quest, Captain Toad visits many different levels to collect diamond, coins and stars.

Each level appears as a page in a story book with specific goals to complete. Each stage has three hidden diamond to collect and one special objective, such as collecting a golden mushroom, avoiding or defeating all the enemies, or gathering a set number of coins, to complete. The main objective is to reach the golden star at the end of the levels. To do so, the player controls Captain Toad (or Toadette) through mazes, platforms and tunnels. Completed objectives are then checked on the storybook page, and a stamp appears once all objectives are met.

Captain Toad cannot jump, but he can pick-up and use turnips and other tools, like a pickax that defeats the enemies and destroys the blocks in Captain Toad's way for a limited time or a cherry that creates a duplicate Captain Toad. The WiiU GamePad is used in different ways to help Captain Toad move around: tilting the GamePad (or using the right analog) changes the view to help spot hidden objects, some parts of the level can be rotated, raised or lowered by touching them on the GamePad screen, and some wheels can be turned via the touch screen to rotate certain platforms. If Captain Toad gets hurt, he shrinks down, and regains his normal size if he uses a mushroom. If he gets hurt a second time, he loses a life; if all lives are lost, it's game over. Finding a 1-up mushroom or collecting 100 coins adds an additional life.

In some levels, Captain Toad rides a mine cart and the player must shoot at coins, blocks, enemies and treasures as the cart moves towards the golden star.

In the later 3DS and Switch version, the bonus levels based on Super Mario 3D World were replaced with new levels based upon worlds from Super Mario Odyssey, including levels which could be unlocked using the 3 Super Mario Odyssey Wedding Amiibo's. Additionally, after failing a level a set amount of times a invincibility mushroom will appear to aid in passing the level.