Preheat oven to 450°F. Partially bake your pie crust: line the bottom of the chilled crust with parchment paper and pie weights. Bake for 8 minutes, then carefully remove parchment and weights. Poke holes in the bottom with a fork and bake again for 5 minutes. Lower the oven temperature to 325°F. (See notes.)
Meanwhile, cook bacon over medium heat in a large skillet. Cook until crispy, then reserve fat and drain on paper towels and crumble.
Cook onion in some of bacon fat until tender and translucent, about 3-5 minutes over medium heat in the same skillet.
Toss cheese with flour. Set aside.
Whisk eggs, milk, half and half, and salt. Stir in bacon, onions, and cheese. Add to hot crust.
Place pie on a cookie sheet and cover with a pie shield.
Bake for an additional 45-50 minutes or until the center is slightly wobbly (not rolling when tapped) and the egg looks very light golden.
Cool at least 1 hour before slicing and serving.
Store leftovers in the refrigerator in an airtight container.