Preheat the oven to 375°F (190°C).
Heat olive oil in a large skillet over medium heat.
Add chopped onion and minced garlic to the skillet and sauté for 3-4 minutes until softened.
Add ground turkey to the skillet and cook, breaking it apart with a spoon, until browned and cooked through, about 6-8 minutes.
Stir in diced zucchini, diced tomatoes, dried Italian seasoning, salt, black pepper, and crushed red pepper flakes. Cook for an additional 5 minutes until vegetables are tender and mixture is well combined.
Remove skillet from heat and stir in half of the shredded mozzarella cheese and all of the grated Parmesan cheese.
Place the prepared bell peppers upright in a baking dish.
Spoon the turkey mixture evenly into each bell pepper, filling them completely.
Sprinkle the remaining mozzarella cheese on top of each stuffed pepper.
Cover the baking dish with aluminum foil and bake for 30 minutes.
Remove the foil and bake for an additional 10 minutes until the cheese is melted and bubbly.
Remove from oven and let cool for 5 minutes before serving.