Preheat the oven to 375F. Chop the bell pepper into 1-inch pieces, finely dice the onion, and mince the jalapeño.
Heat a large skillet over medium-high heat. I like to use my cast iron skillet for this. Drizzle with oil. Once hot, add the peppers and onion. Cook for 4-6 minutes, until the onion is softened and the bell peppers are starting to brown. Note that the peppers don't soften much more in the casserole.
To a 9x13-inch baking dish add the peppers and onions, rinsed quinoa, drained black beans and lentils, tomatoes, vegetable broth, salsa, chili powder, cumin, smoked paprika, garlic powder, onion powder, and salt. Stir to combine.
Cover tightly with a lid, foil, or an upside down baking sheet. Bake at 375F for 30 minutes. Remove from the oven and stir. The quinoa should be mostly cooked at this point and the casserole will be a little liquidy. If the quinoa isn't cooked through, cover and return to the oven for 5-10 minutes.
Stir ½ cup of cheese into the casserole and sprinkle the remaining cheese on top. Return the casserole to the oven to bake, uncovered, for 10-15 minutes. The casserole is ready when it's bubbling and the cheese is melted.
Let rest for 5 minutes before serving. Enjoy garnished with cilantro and additional salsa.
Notes
Salsa: This is a major flavor enhancer and it contributes some of the cooking liquid. Any type of tomato-based should work here.
Salt: Adjust to taste based on the saltiness of the salsa. I actually forgot the salt the first time I baked this and I didn't even notice because the salsa was very salty.
Optionally, you can speed up the total cooking time by 5-10 minutes by bringing the liquids to a simmer on the stovetop before adding them to the casserole dish.
Reheating: Reheat individual portions in the microwave. Reheat the entire casserole in the oven at 325F for 20-30 minutes, or until warmed through. Cover with foil if the casserole starts to dry out too much.
Freezing: This freezes well as a full casserole or as individual slices. Cover the casserole in plastic wrap and foil or plastic wrap and a lid before freezing. If reheating in the oven, add an extra 15 minutes to the reheat time (30-45 minutes total). The casserole can also thaw overnight in the fridge.