Preheat oven to 375°F. Sauté onion and garlic in oil until soft, 3–4 minutes.
Stir in quinoa, beans, corn, cumin, chili powder, salt, and pepper; heat through. Fold in half the cheese.
Stuff peppers with filling, top with remaining cheese, place in a baking dish with 1/4 cup water, cover, and bake 25–30 minutes until peppers are tender.
While peppers bake, chop reserved pepper tops and simmer in broth 10 minutes for a quick soup; season to taste.
Serve peppers hot with a ladle of the pepper-top soup on the side.