Place bacon in a large, deep skillet. Cook over medium high heat until evenly brown. Drain (reserving 1 tablespoon 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 for 45 minutes, or until lightly brown on top and firm in the middle. Serve warm.