Add quinoa and onion to a large saucepan with 2 cups of water and a pinch of salt. Bring to a boil over medium-high heat. Boil 5 minutes, cover, turn off heat and let steam 15 minutes. Fluff with a fork.
In the meantime, microwave pepper halves 2-3 minutes to soften slightly. (Prepared this way, the peppers should come out crisp-tender. If you want them crisper, you can omit this step.).
Pour quinoa/onion mixture into a mixing bowl. Stir in black beans, tomato, green chiles and their juices, cilantro, 1/4 tsp salt, and 1/4 tsp pepper. If the mixture seems to dry, drizzle in a bit of olive oil (I didn’t need any).
Pour enchilada sauce into a 9×13″ baking dish. Divide filling among peppers. Nestle stuffed peppers into the enchilada sauce. Sprinkle with cheeses.
Cover the pan with foil and bake at 375 degrees 25-30 minutes. Remove foil and cook about 5 minutes longer. Serve peppers drizzled with enchilada sauce.