Preheat oven to 350º. Place bacon in a large skillet. Cook over medium high heat until evenly brown. Drain (reserve 1 T. of grease). Crumble bacon and set aside.
Heat reserved bacon grease in skillet and saute onion until soft. In a large bowl, beat together eggs, milk, flour, parsley, thyme, salt and pepper. Add bacon, onion, mozzarella and cheddar cheese. Mix well.
Pour mixture into pie crust. Bake in preheated oven until lightly brown on top and firm in the middle. About 40 minutes. Serve warm.