Prep the oven and pan: Preheat your oven to 400°F (200°C).
Line a baking sheet with parchment for easy cleanup.
Clean the mushrooms: Wipe the caps with a damp paper towel. Twist off stems and use a small spoon to scrape out the gills if using larger caps. This creates more room for filling and reduces excess moisture.
Season and pre-bake: Place the caps hollow-side up on the baking sheet.
Brush with 1 tablespoon olive oil and sprinkle with salt and pepper. Bake for 8–10 minutes until they release some liquid. Carefully drain off any moisture from the pan.
Make the filling: In a bowl, mix the marinara, Italian seasoning, red pepper flakes (if using), and half the Parmesan.
Taste and adjust salt if needed.
Assemble: Spoon a little sauce into each cap—just enough to lightly coat the bottom. Add a layer of mozzarella, then scatter pepperoni, peppers, and onion. Top with remaining mozzarella and the rest of the Parmesan.
Drizzle with the remaining 1 tablespoon olive oil.
Bake: Return to the oven for 10–12 minutes, or until the cheese is melted and golden around the edges. For extra browning, broil for 1–2 minutes, watching closely.
Finish and serve: Let the mushrooms rest 3–5 minutes to set. Top with torn basil and a crack of black pepper.
Serve warm.