Prep the peppers: Heat the oven to 400°F (200°C).
Slice the tops off the bell peppers and remove seeds and membranes. If they don’t stand upright, trim a thin slice from the bottoms to level.
Soften the peppers: Place peppers cut-side up in a baking dish. Brush or spray lightly with olive oil and sprinkle with salt.
Roast for 12–15 minutes to soften slightly. Set aside.
Sauté aromatics: In a skillet over medium heat, warm 1 tablespoon olive oil. Add onion and a pinch of salt.
Cook 4–5 minutes until translucent. Stir in garlic for 30 seconds until fragrant.
Build the base: Add diced tomatoes and tomato paste to the skillet. Stir in smoked paprika, Italian seasoning, and red pepper flakes if using.
Simmer 2–3 minutes to thicken. Remove from heat.
Make the protein mix: In a large bowl, combine shredded chicken, cooked rice or quinoa, cottage cheese, Greek yogurt, 1/2 cup mozzarella, and Parmesan. Add the tomato-onion mixture.
Season with salt and black pepper. Mix until evenly combined.
Stuff the peppers: Spoon the filling into the pre-roasted peppers, packing firmly and slightly mounding on top. Sprinkle the remaining 1/2 cup mozzarella over the stuffed peppers.
Bake: Pour a splash of water (about 1/4 cup) into the bottom of the baking dish to help steam.
Cover loosely with foil and bake 15 minutes. Remove foil and bake another 10–12 minutes until cheese is melted and lightly golden.
Finish and serve: Let peppers rest 5 minutes. Garnish with chopped parsley or basil.
Taste and add a final pinch of salt or pepper if needed.