There are a few ways you can restore energy in Echoes of Wisdom. The main way is by exploring the Still World.
As you wander around inside the rifts and the dungeons, you'll see little blue crystals floating around. Walk close to them and Zelda will automatically absorb them to restore your energy.
Rift enemies — also known as shadow enemies or echo enemies — also drop energy. These can be found near rifts on the overworld or inside many of the game's rifts. Other ways to restore energy are by finding Might Crystals or by drinking certain Smoothies.