Bring a large pot of salted water to a boil. Add the penne pasta and cook according to package instructions until al dente, usually about 10-12 minutes. Drain the pasta and set aside.
Heat a large skillet over medium heat. Add the ground beef and cook until browned, breaking it up with a wooden spoon. Drain any excess fat if needed. Add the chopped onion and minced garlic to the skillet and sauté until the onion is translucent and fragrant, about 3-4 minutes.
Stir in the crushed tomatoes, tomato paste, dried oregano, dried basil, salt, and black pepper. Let the sauce simmer for 10 minutes, stirring occasionally to let the flavors meld and the sauce thicken slightly.
Add the cooked penne pasta and turkey pepperoni slices to the skillet. Stir well to ensure the pasta is fully coated with the sauce and evenly mixed with the pepperoni.
Preheat your oven to 375°F (190°C). Transfer the pasta mixture to a baking dish. Sprinkle the shredded mozzarella cheese evenly on top, followed by the grated Parmesan cheese.
Place the baking dish in the oven and bake for 20-25 minutes or until the cheese is melted, bubbly, and golden brown on top.
Remove from the oven and let it cool for a few minutes before serving. The cheesy, saucy goodness of this Deep-Dish Pepperoni Pizza Pasta is now ready to be devoured!