The player may choose between two different game modes from the game's main menu: Story Mode and Trial Mode. Upon entering either mode, the player can select a course, find out which fruit will be the Lucky Fruit, and choose a Yoshi of desired color to play as. Trial Mode is devoid of courses to play at the start of the game, as these have to be unlocked by completing them in Story Mode.
On each course, the goal is to fill the Fruit Frame by eating 30 pieces of fruit.[4][5] These may be found in abundance throughout every course, lying around, floating in bubbles, and even carried by some enemies. The puzzle element of the game encourages the player to apply strategy to achieve a high score. For instance, the player gains more points from eating one kind of a fruit in a row, and even more so if the fruit is a Favorite Fruit or a Lucky Fruit. In addition, valuable secrets are hidden throughout every course that will contribute to the total score.
The courses are spread across six pages, containing four courses each. The courses are sorted by difficulty, and the choice of which course to play is made individually for each page. While the first page will always display four courses, the following pages will initially be limited to only one course. In order to unlock the remaining courses, the player must seek out and collect Special Hearts (not to be confused with the Heart Fruit).[5] Each course has three collectable hearts, and the number of hearts collected determines the number of additional courses that are unlocked on the following page. For example, if the player collects two hearts during a course, they will be allowed to choose from course 1, 2, and 3 on the next page.[4]
The abilities of Yoshis include running, ducking, jumping, ground pounding, temporary hovering, and hurling eggs. Eggs no longer ricochet off walls and the ground, and Yoshis no longer have the option of spitting out enemies, which are turned into eggs as soon as they are swallowed.