Preheat the oven to 375°F (190°C).
Cut the tops off the bell peppers and remove the seeds and membranes. Set aside.
In a large skillet, heat some olive oil over medium heat. Add the diced eggplant, zucchini, yellow squash, and red onion. Cook until the vegetables are tender, about 8-10 minutes.
Add the minced garlic and cook for an additional 1 minute.
Stir in the diced tomatoes, dried basil, dried oregano, dried thyme, salt, and pepper. Cook for 5 minutes, stirring occasionally.
Remove from heat and stir in the cooked wild rice.
Fill each bell pepper with the ratatouille mixture and place them in a baking dish.
Cover the baking dish with aluminum foil and bake for 30 minutes.
Remove the foil and continue baking for an additional 10-15 minutes, until the peppers are tender and the filling is heated through.
Serve hot and enjoy!