Preheat the oven to 375°F.
In a large skillet over medium heat, add the olive oil. Once hot, add the diced onion and sauté for about 3 minutes until translucent. Add the minced garlic and cook for an additional minute.
Add the Italian sausage to the skillet, breaking it apart with a spoon. Cook until browned and cooked through, about 5-7 minutes. Drain any excess fat.
Stir in the orzo, diced tomatoes, Italian seasoning, salt, and black pepper. Cook for another 2-3 minutes, allowing the flavors to meld. Remove from heat and stir in half of the mozzarella cheese.
While the filling is cooling slightly, prepare the bell peppers. Cut the tops off the peppers and remove the seeds and membranes. Place them upright in a baking dish.
Spoon the sausage and orzo mixture into each bell pepper, packing it down gently. Top each stuffed pepper with the remaining mozzarella cheese and sprinkle with Parmesan cheese.
Cover the baking dish with aluminum foil and bake for 25 minutes. Remove the foil and bake for an additional 10-15 minutes, or until the cheese is bubbly and golden.
Let the stuffed peppers cool for a few minutes before serving. Garnish with fresh basil leaves if desired.