Preheat and prep the pan: Heat your oven to 375°F (190°C). Lightly oil a baking dish large enough to fit the peppers upright.
Add a few tablespoons of water or broth to the bottom to help steam as they bake.
Cook the quinoa: Rinse 1 cup of quinoa under cool water until it stops foaming. Combine with 2 cups of water and a pinch of salt in a pot. Bring to a boil, then cover and simmer 15 minutes.
Turn off heat and let it sit, covered, 5 minutes. Fluff with a fork.
Prepare the peppers: Slice off the tops and remove seeds and membranes. If a pepper won’t stand upright, trim a thin slice off the bottom to level it.
Place them in the prepared dish, open side up.
Sauté the aromatics: Warm 2 tablespoons olive oil in a large skillet over medium heat. Add chopped onion and a pinch of salt. Cook 4–5 minutes until translucent.
Stir in garlic and cook 30 seconds until fragrant.
Add vegetables and spices: Stir in diced zucchini, cumin, smoked paprika, oregano, and red pepper flakes if using. Cook 3–4 minutes until the zucchini softens slightly.
Build the filling: Add drained diced tomatoes, tomato paste, corn, black beans, and 1/2 cup vegetable broth. Simmer 3–4 minutes to meld flavors.
Fold in the cooked quinoa. Taste and season with salt and black pepper. The mixture should be moist but not soupy.
Cheese it up (optional): Stir in half the shredded cheese to create a creamy, cohesive filling.
Reserve the rest for topping.
Stuff the peppers: Spoon the filling evenly into the peppers, mounding slightly. Sprinkle remaining cheese over the top.
Bake: Cover the dish loosely with foil. Bake 25 minutes.
Remove foil and bake another 10–15 minutes, until the peppers are tender and the cheese is bubbly and golden.
Finish and serve: Let the peppers rest 5 minutes. Garnish with chopped cilantro or parsley. Serve with lime wedges for a fresh, bright finish.