Preheat oven to 400 degrees. Line a 9 inch quiche dish with the pastry and flute the edges. Fill with dry beans and bake for 15 minutes or until light brown. Discard the beans and cool on a rack.
Meanwhile, in a 6 inch nonstick skillet, melt the butter over moderately high heat. Add the onion and saute for 5 minutes or until soft and then transfer to a medium size bowl. Toss with the cheese, bacon and flour. Spread in the pie crust.
In the same bowl, whisk the eggs with the milk, salt and nutmeg. Pour over the pie mixture and bake, uncovered for 35 minutes or until the center is set.