Heat 2 tablespoons of the oil in a large skillet. Add the onions and cook over low heat, stirring often, until meltingly soft and deep golden, about 30 minutes; add a little bit of water as the onions begin to look dry. Season with salt and pepper and transfer to a plate.
Heat the remaining 1 tablespoon of oil in a large saucepan. Add the quinoa and cook over high heat, stirring, until light golden and fragrant, 3 to 4 minutes. Add the water and 3/4 teaspoon of salt and bring to a boil. Cover and cook over low heat until all of the water has been absorbed and the grains are tender, 12 to 15 minutes. Fluff the quinoa with a fork and stir in the onions. Season with salt and pepper. Transfer the quinoa to a bowl and serve at once.