Depiction in the seriesseason four's two-part premiere, Twilight Sparkle experiences a flashback where she learns that Princess Celestia and Princess Luna discovered the Tree of Harmony a thousand years ago. The princesses took the Elements of Harmony from the tree and used their magic to defeat Discord.
According to Celestia, the tree controls and contains all that grows in the Everfree Forest, even without the Elements in it.
Twilight Sparkle and her friends discover that the Tree of Harmony has lost its magic, allowing Discord's plunderseeds to sprout and grow all over the Everfree Forest, slowly killing the tree. Twilight and her friends give up the Elements of Harmony and return them to the tree, recharging its magic and restoring the forest.When the Tree of Harmony regains its magic, a flower sprouts at its roots. The flower blooms to reveal a chest with six locks. Princess Celestia tells Twilight that she doesn't know where the keys are. Celestia assures Twilight that it is a mystery she will not be solving alone.
The tree is seen again with the Elements of Harmony still on its branches with the mysterious chest in front of it. At the episode's climax, the tree activates the elements and connects them with the rainbow power that came from the chest. The tree then transports the chest into the ground in Ponyville, which sprouts into Twilight's new castle. The new castle partly resembles the tree itself.
In the season seven finale, it is revealed that the Tree of Harmony first grew from a seed planted by the Pillars of Old Equestria and imbued with the elements within them so that it would protect Equestria from darkness in their absence. After returning from limbo, Star Swirl the Bearded removes the Elements of Harmony from the Tree in order to banish the Pony of Shadows.
In The Journal of the Two Sisters, Star Swirl the Bearded shows the tree to a young Luna and Celestia. The tree had the three cutie marks before Celestia and Luna received theirs. It is implied that Star Swirl knew that Twilight was going to get the third cutie mark.
The tree is used in Gameloft's mobile game.