Prepare the peppers:
Preheat your oven to 375°F (190°C). Cut the tops off the bell peppers and remove the seeds and membranes. Lightly season the insides with a pinch of salt and place them upright in a baking dish.
Cook the filling:
Heat a large skillet over medium heat. Add the ground beef or sausage and cook until browned. Drain excess fat if necessary. Add the onion and garlic, cooking until softened and fragrant. Stir in the marinara sauce, Italian seasoning, red pepper flakes, salt, and pepper. Cook for another 2-3 minutes. Remove from heat and mix in the cooked rice.
Stuff the peppers:
Spoon the filling mixture into each bell pepper, packing it gently to fill completely. Top with a mixture of mozzarella and Parmesan cheese.
Bake the peppers:
Cover the baking dish with aluminum foil and bake for 25-30 minutes. Remove the foil and bake for an additional 10-15 minutes, or until the peppers are tender and the cheese is melted and bubbly.
Serve:
Remove the stuffed peppers from the oven and let them cool slightly. Garnish with fresh basil or parsley before serving.