Preheat the oven to 375°F (190°C).
Bring a large pot of water to a boil. Add the bell peppers and boil for 5 minutes to soften slightly. Remove and drain well.
Heat olive oil in a large skillet over medium heat. Add the chopped onion and cook for 3-4 minutes until softened.
Add minced garlic to the skillet and cook for 1 minute until fragrant.
Add ground beef to the skillet and cook until browned, breaking it apart with a spoon, about 6-8 minutes. Drain any excess fat.
Stir in cooked rice, dried oregano, dried basil, salt, and black pepper. Mix well and cook for 2 more minutes. Remove from heat.
In a medium bowl, combine crushed tomatoes, tomato paste, sugar, dried thyme, salt, and black pepper. Stir well to make the tomato sauce.
Place the bell peppers upright in a baking dish. Spoon the beef and rice mixture evenly into each bell pepper.
Pour half of the tomato sauce over the stuffed peppers and around them in the baking dish.
Cover the baking dish with aluminum foil and bake in the preheated oven for 35 minutes.
Remove the foil and sprinkle shredded mozzarella cheese on top of each stuffed pepper.
Return to the oven and bake uncovered for an additional 10-15 minutes, until the cheese is melted and bubbly.
Remove from oven and spoon the remaining tomato sauce over the stuffed peppers before serving.