Rinse 1 cup of dry quinoa under cold water to remove its natural bitterness. In a medium saucepan, combine quinoa with 2 cups of water and bring to a boil. Lower the heat, cover, and simmer for about 15 minutes, or until the water is absorbed and quinoa is tender. Fluff with a fork and set aside.
While quinoa is cooking, heat a small amount of oil in a large skillet over medium heat. Add the chopped yellow onion and sauté until softened and translucent, about 5 minutes.
In a large mixing bowl, combine cooked quinoa, sautéed onions, and the drained and rinsed black beans. Mix gently to combine without mashing the beans.
Lightly warm the corn tortillas in the skillet for 20-30 seconds on each side to make them pliable and less likely to tear when rolling.
Preheat your oven to 375°F (190°C). Spread a thin layer of enchilada sauce on the bottom of your baking dish. Spoon about 1/4 cup of the quinoa and black bean filling onto each tortilla, sprinkle a little shredded cheese over the filling, then roll tightly and place seam-side down in the dish. Repeat with all tortillas.
Pour the remaining enchilada sauce evenly over the rolled tortillas. Sprinkle the remaining shredded cheese on top. Cover the dish with foil and bake for 20 minutes. Remove the foil and bake for another 10 minutes until cheese is bubbly and slightly browned.
Once out of the oven, sprinkle chopped green onions over the enchiladas and serve with lime wedges on the side.