Yoshi's Island made Yoshi the main playable character for the first time in a Mario game. At the beginning of each level, Baby Mario is passed between different-colored Yoshis. All the Yoshis have the same range of moves, such as stomps and tongue-licks. If the player holds down the jump button the Yoshis pedal their feet furiously in the air to achieve a floating effect; this allows them to stay airborne for a couple of seconds and gain a little extra height. This floating maneuver may be performed multiple times if necessary.

Yoshis can collect eggs during their travels across the levels by utilising their unique metabolism to instantaneously digest enemies that they had swallowed. These eggs (up to six at a time) follow Yoshi along until they were thrown. Many of the game's puzzles involve bouncing eggs around the levels or skimming them over water to hit distant enemies or objects. In addition to eggs, Yoshi may also collect keys to open locked doors. Finally, duck-like creatures (called Huffin' Puffins) exist in a few levels; these travel a short distance then return to you.

Unlike other platform games in the Mario series, the player's character can be attacked an unlimited number of times by most enemies without harm. Whenever Yoshi is hit by an enemy, Baby Mario flies off his back, floating around the level in a bubble and wailing loudly as a countdown timer begins. If the countdown reaches zero before Yoshi tags the bubble, Kamek's servants capture Mario and the player loses a life. At the beginning of each level, the countdown timer begins at ten; the player can add time to the countdown to a maximum of thirty by collecting stars in each stage. If Yoshi rescues Baby Mario by touching the bubble when the countdown is less than ten, the timer is slowly replenished back to ten as long as Mario remains on Yoshi's back.

At the end of each level, the player jumps through a 'roulette' ring and the level is scored. The player earns points based on three criteria:

Every star, remaining on the countdown timer is worth one point. Up to thirty stars can be collected.

Scattered among the coins in each level are twenty special red coins; each one collected is worth one point.

Hidden throughout each stage are five flowers; each one collected is worth ten points, and for every flower collected you have another flower displayed on the roulette ring.