Preheat the oven to 375 degrees Fahrenheit, and prepare the 4 boneless skinless chicken breasts by patting them off and cutting a pocket into each one. Set aside.
Heat 1 tablespoon olive oil in a skillet over medium-high heat, add the 2 minced shallots, and cook for 3 minutes, stirring frequently. Add the 2 cloves minced garlic and 3 cups chopped spinach, and cook until the spinach has wilted. Remove from heat.
In a small bowl, mix the 1 teaspoon oregano, 1 teaspoon thyme, ½ teaspoon salt, ½ teaspoon ground black pepper, and ½ teaspoon red pepper flakes. Divide this mixture in half.
In a medium bowl, add the 4 ounces softened cream cheese, 1 cup freshly grated parmesan cheese, cooked spinach and shallots, and half of the spice mix. Mix well to combine.
Rub the 2 tablespoons olive oil onto each chicken breast and season them with the remaining spice mix. Stuff each chicken evenly with the spinach and cream cheese mixture until it has all been used.
Place the stuffed breasts onto a 9X13 inch baking dish. Bake uncovered for 30-45 minutes, or until the chicken is cooked through and there is a nice brown crust on the top of each one.