Preheat oven to 400 degrees. Prick bottom of the crust with a fork in several places. Partially bake crust for 15 minutes. Remove from oven and keep warm.
Fry the bacon in a medium skillet over medium heat until crisp, about 8 minutes. Drain on paper towels and finely chop. Reserve the fat in the skillet.
Return skillet to medium heat. Add the onion and cook until softened, about 5 minutes. Toss the onion with the chopped bacon in a small bowl and set aside.
In a large bowl, whisk together the eggs, milk, cream, thyme, 1/2 teaspoon of pepper, and 1/4 teaspoon of salt.
Reduce the oven temperature to 350 degrees and adjust an oven rack to the middle position. Set pie crust on a rimmed baking sheet. Sprinkle the cheese and then the bacon-onion mixture evenly over the bottom of the warm pie crust.
Slide the middle oven rack out and set the baking sheet with the pie crust on it. Carefully pour the egg mixture evenly into the pie shell until it reaches 1/2 inch from the top of the crust. Slide the entire baking sheet with the quiche in to the oven.
Bake until the top of the quiche is lightly browned and a knife inserted about 1 inch from the edge of the crust comes out clean, about 40 to 50 minutes. (The center should be soft, but still set, similar to gelatin).
Transfer the quiche to a baking rack to cool for 5 minutes. Serve warm, cold, or at room temperature.