The gameplay in Land Before Time: Into the Mysterious Beyond offers a diverse range of experiences as players control each of the five dinosaurs. Each character has its unique level type, allowing for varied gameplay. Littlefoot excels at normal platforming, while Petrie soars through the skies on his wings. Ducky dives into the depths to swim and navigate underwater levels. Cera's strength comes in handy when breaking boulders, and Spike navigates complex mazes.
However, not all levels are played solo – some special stages bring together all five dinosaurs as they ride a leaf sled or a raft through treacherous terrain. The final level sees a greater emphasis on combat as players take control of Littlefoot's grandfather, adding an extra layer of challenge to the game.