Preheat oven to 375°F (190°C).
Cook the penne pasta according to package instructions until al dente. Drain and set aside.
Heat olive oil in a large skillet over medium heat. Add the diced onion and sauté for 3-4 minutes until translucent.
Add the Italian sausage to the skillet, breaking it up with a spoon. Cook for 6-8 minutes until browned and cooked through.
Add the minced garlic to the skillet and cook for 1 minute until fragrant.
Stir in the marinara sauce, diced tomatoes, dried Italian seasoning, crushed red pepper flakes, salt, and black pepper. Simmer for 5 minutes to combine flavors.
In a large mixing bowl, combine the cooked pasta and sausage sauce mixture. Stir until well combined.
Transfer half of the pasta mixture into a 9×13-inch baking dish. Sprinkle half of the mozzarella and Parmesan cheeses over the pasta.
Add the remaining pasta mixture on top, then sprinkle with the remaining mozzarella and Parmesan cheeses.
Cover the baking dish with aluminum foil and refrigerate if making ahead, up to 24 hours.
When ready to bake, remove the foil and bake uncovered for 25-30 minutes until the cheese is melted and bubbly.
Remove from oven and let rest for 5 minutes. Garnish with chopped fresh parsley before serving.