Tree Flutes were created by the people of Ayuthay, and influences their architectural design. Tree Flutes generally serve to open various entrances and trigger certain events. Most doors that are triggered by the Tree Flute are stone doors that are opened via large trees and vines. When used at the Ancient Tree, it reveals a secret entrance to the underground portions of the cities. In addition, a secret door is opened by Amiti that leads to the throne room of Ayuthay's palace.
Later on, the Tree Flute awakens the Sand Prince, starting a boss battle. Later on, the Tree Flute, combined with the Insight Psynergy, opens the true entrance to the Ouroboros labyrinth. After this, the Tree Flute has little use, but remains in the player's possession, as it cannot be sold.