Where is My Heart? is a 2D puzzle platformer about three forest spirits (coloured brown, orange and black) who are lost in the forest. The player has to help them piece back together the environment so they can get home to the tree where they live. The game consists of 26 single screen levels. They are completed when the three spirits reach the magical tree.
The three spirits always appear at the start of the level and are controlled separately by switching between them. They are all able to move around and jump. They can stand on top of each other to reach platforms and buttons can make blocks and platforms appear in the environment. In specific locations they can form a tower of three spirits and the one at the top then transforms into a magical creature with a specific ability. The brown spirit becomes Antler Ancestor who can double jump. The orange spirit becomes Rainbow Spirit and can rotate the world. The black spirit becomes Bat King and is able to illuminate the environment to reveal platforms only visible to it.
The most prominent puzzle element of the game is that the level is split up in several comic-book panels. These form a single environment, but are often not in the right order and all over the screen. Even though they are apart, the logical sequence of the panels is maintained, meaning that if a character exists a panel to the right, it will appear in the next panel following the logical order, regardless of the position of the panel on the screen. The most difficult puzzles are used in conjunction with the orange spirit’s ability to rotate the world. The character can jump, freeze in the air and then rotate the world to continue in another panel, even if that would be logically impossible. If the character is released outside of a panel or if any character falls down a gap, it dies immediately but restarts from the beginning.
Next to merely completing a level, it is possible to finish it in a better way by collecting all hearts along the way. There is also a perfect way to complete a level by collecting all hearts without dying once. Levels are unlocked one after another, but by perfecting them it is possible to reveal some earlier.