Preheat oven to 375°. Parcook the bacon slices by frying them for 2 to 3 minutes. Remove bacon from the skillet and drain on paper towels.

Spray a metal muffin pan with cooking spray. Taking one slice of bacon at a time, wrap the inside of a muffin cup to create a ring. Repeat with the remaining slices of bacon (2 slices of bacon per muffin cup).

Carefully crack one egg into each bacon-lined cup. Sprinkle each egg with thyme leaves, Parmesan cheese, salt, and pepper. Bake the egg cups for 10 to 15 minutes, until the centers have set. You can adjust the cooking time based on how you prefer the consistency of your egg yolks.