Cook the sausage. Heat a large skillet over medium heat. Add sausage and cook, breaking it up with a spoon, until browned and cooked through, 6–8 minutes. If the pan is dry, add olive oil.
Sauté the veggies. Add onion, bell pepper, and mushrooms to the skillet.
Cook until softened and most of the moisture cooks off, about 5–7 minutes. Stir in garlic and cook 30 seconds until fragrant.
Add sauce and seasonings. Pour in the marinara, Italian seasoning, and red pepper flakes. Stir and simmer 2–3 minutes.
Taste and season with salt and black pepper.
Assemble the bowls. Divide the saucy meat-and-veg mixture among 4 meal prep containers or oven-safe bowls. Top each with mozzarella and a sprinkle of Parmesan. Add pepperoni slices and olives on top.
Melt the cheese. For meal prep: let cool, cover, and refrigerate.
Reheat later until hot and bubbly. For immediate eating: Broil bowls for 2–3 minutes until the cheese melts and browns slightly, or microwave 1–2 minutes.
Finish and serve. Garnish with chopped basil or parsley. Enjoy as is or with a simple side salad.