Preheat oven to 425 degrees F.
Slice the bell peppers in half vertically, through the stem, and remove seeds and membranes. Drizzle on about 1 tablespoon olive oil and season with ½ teaspoon kosher salt and ¼ teaspoon black pepper.
Use your hands to rub the oil and seasoning all over the peppers, and place them cut-side up in a baking dish. Bake peppers for 20 minutes.
Heat remaining 2 olive oil in a large skillet over medium heat. Add onion and sauté for 4 to 5 minutes, until softened. Stir in garlic and cook for 30 seconds until fragrant.
Pour in the diced tomatoes (with their juices), and the rest of the salt and pepper, along with ground cumin, smoked paprika and chili powder. Stir to combine and bring to a simmer for 5 to 7 minutes, until the mixture starts to thicken and the flavors meld.
Add in black beans and corn. Stir to combine and turn off heat. Fold in cooked quinoa, juice of ½ a lime and fresh chopped cilantro.
Spoon the filling evenly into the bell peppers. Sprinkle the top of the peppers with about 1 tablespoon each of shredded mozzarella.
Cover the dish with foil and bake for 20 minutes. Remove foil and bake an additional 10 minutes, or until the peppers are tender and cheese is melted and bubbly.
Garnish with more fresh, chopped cilantro (optional) and serve warm.