Preheat and prep: Heat your oven to 375°F (190°C).
Grease a 9x9-inch (or similar) baking dish with a light coat of olive oil.
Cook the meat: In a large skillet, warm 1 tablespoon olive oil over medium heat. Add the ground meat, season with salt and pepper, and cook until browned, breaking it up as it cooks. Drain excess fat if needed.
Add aromatics: Stir in the garlic and Italian seasoning.
Cook for 30–60 seconds until fragrant. If using red pepper flakes, add them now.
Sauté the veggies: Push the meat to one side of the skillet. Add the remaining 1 tablespoon olive oil, then the mushrooms, bell pepper, and onion.
Sauté 3–4 minutes until slightly softened.
Wilt the greens: Add the spinach to the skillet and cook until just wilted. Taste and adjust salt and pepper.
Stir in the sauce: Pour in the low-carb marinara and mix everything together. Let it simmer for 2–3 minutes to thicken slightly.
Layer in the dish: Spread the mixture evenly in the baking dish.
Sprinkle half the mozzarella and half the Parmesan on top.
Add toppings: Scatter the black olives and arrange the pepperoni slices. Top with the remaining mozzarella and Parmesan for maximum melt and browning.
Bake: Place the dish in the oven and bake for 18–22 minutes, until the cheese is melted and bubbling with golden spots.
Rest and serve: Let the casserole rest for 5–10 minutes so it sets. Garnish with fresh basil if you like.
Slice and serve warm.