Place chicken pieces in a bowl and pour in the marinara sauce and a pinch of salt and pepper and marinate in the refrigerator for 30 minutes.
Meanwhile, in a sauté pan add 1 tbsp of the oil and the shallots, thyme and a pinch of salt and cook for 4 minutes and then add in the garlic and cook another 2 minutes.
Next, add in the mushrooms and marinated chicken pieces, a pinch more salt and pepper and cook for about 7 minutes but not cooked all the way through.
Next, add the peppers to a baking dish and coat the bottom and rub the peppers with the rest of the olive oil. Then add in some parmesan cheese and the toasted pine nuts to the chicken mixture and mix well.
Last, fill each pepper with the chicken mixture and top with the mozzarella cheese. Bake covered with foil at 375 degrees for about 30 minutes and then take off the foil and cook for another 5 minutes and enjoy! :)