Preheat and prep. Heat the oven to 375°F (190°C). Grease a 9x13-inch baking dish or a similar casserole dish.
Brown the meat. Heat olive oil in a large skillet over medium-high.
Add the ground meat and cook, breaking it apart, until browned and cooked through. Season with salt and pepper.
Sauté the aromatics. Add diced onion and minced garlic to the skillet. Cook 2–3 minutes, just until fragrant and softened.
Add veggies. Stir in bell peppers and mushrooms.
Cook another 4–5 minutes to soften and release moisture. If there’s excess liquid, let it cook off so the casserole isn’t watery.
Season and sauce. Stir in Italian seasoning and red pepper flakes. Pour in the low-sugar marinara and simmer for 2–3 minutes.
Taste and adjust salt and pepper.
Assemble the base. Spread the meat-veggie mixture evenly in the baking dish. Sprinkle half the mozzarella over the top.
Add toppings. Layer sliced olives and half the pepperoni over the cheese. Scatter the remaining mozzarella and the Parmesan on top.
Finish with the rest of the pepperoni.
Bake. Bake uncovered for 18–22 minutes, until the cheese is melted, bubbly, and lightly golden at the edges.
Rest and garnish. Let the casserole rest for 5–10 minutes to set. Garnish with chopped basil or parsley. Slice and serve.