Heat the oven. Preheat to 400°F (200°C). Lightly oil a 9x13-inch baking dish or similar pan.
Prep the peppers. Slice the bell peppers in half lengthwise and remove seeds and membranes.
Brush or rub the insides with olive oil and a pinch of salt. Place them cut-side up in the baking dish.
Soften the peppers (optional but helpful). For softer peppers, bake them empty for 10 minutes while you make the filling. This jump-starts the cook time.
Make the filling base. In a large bowl, combine the softened cream cheese, 1 cup marinara, garlic, Italian seasoning, red pepper flakes (if using), 1/2 teaspoon salt, and a few grinds of black pepper.
Stir until smooth.
Add the chicken and cheese. Fold in the shredded chicken, 1 cup mozzarella, and 1/4 cup Parmesan. The mixture should be thick and creamy.
Stuff the peppers. Spoon the filling evenly into the pepper halves, mounding slightly. Don’t overpack to the point of spilling.
Top with sauce and cheese. Spoon a thin layer of marinara (about 1–2 tablespoons) over each stuffed pepper.
Sprinkle the remaining mozzarella and Parmesan on top.
Bake. Cover the dish loosely with foil and bake for 20 minutes. Remove the foil and bake another 10–15 minutes, until the peppers are tender and the cheese is bubbling and golden in spots.
Finish with herbs. Let the peppers rest for 5 minutes, then sprinkle with chopped basil or parsley for a fresh finish.
Serve. Spoon any pan juices or extra marinara over the peppers. Add a little extra Parmesan if you like.