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.
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.