Preheat your oven to 400°F. Cut the spaghetti squashes in half lengthwise and scoop out the seeds. Drizzle with olive oil and season with salt and pepper. Place cut-side down on a baking sheet and roast for 30-40 minutes until tender.
While the squash is roasting, heat a skillet over medium heat. Add the Italian sausage and cook for 5-7 minutes until browned. Remove and set aside.
In the same skillet, add diced onion, red bell pepper, and yellow bell pepper. Sauté for 5 minutes until soft. Add minced garlic and cook for an additional 1-2 minutes.
In a large bowl, scrape out the spaghetti squash strands. Combine with the sausage and sautéed vegetables. Stir in diced tomatoes, oregano, basil, and red pepper flakes. Season with salt and pepper.
Transfer the mixture to a greased 9x13-inch baking dish. Top with mozzarella and Parmesan cheese. Bake for 20-25 minutes until cheese is melted and bubbly.
Let cool for a few minutes before serving. Garnish with fresh basil if desired.