Preheat (optional). If you want a bubbly, browned top, preheat your oven broiler. If not, you can finish everything on the stove.
Brown the beef. Heat a large oven-safe skillet over medium-high.
Add oil if needed. Add the ground beef and cook, breaking it up with a spatula, until no longer pink, about 5–7 minutes. Season with a pinch of salt and pepper.
Sauté aromatics. Add the diced onion and cook 2–3 minutes until softened.
Stir in the minced garlic and cook 30 seconds until fragrant.
Build the sauce. Reduce heat to medium-low. Stir in the marinara, Italian seasoning, dried oregano, and crushed red pepper flakes. Simmer 2–3 minutes to let flavors meld.
Taste and adjust salt and pepper.
Add veggies and toppings. Fold in the bell pepper, mushrooms, and olives. Let them soften slightly, 2–3 minutes. Stir in half of the pepperoni for extra flavor throughout the skillet.
Cheese it up. Sprinkle mozzarella and provolone evenly over the skillet.
Top with Parmesan and the remaining pepperoni.
Melt and finish. Cover the skillet and cook on low for 3–5 minutes until the cheese is melted. For a browned top, transfer under the broiler for 1–2 minutes, watching closely.
Garnish and serve. Remove from heat and rest 2 minutes. Sprinkle with fresh basil or parsley.
Serve as-is, or spoon over sautéed zucchini ribbons or cauliflower rice.