Preheat oven to 400 degrees. Spray (12) cavities of a standard muffin cup with cooking spray or use silicone muffin cups (I highly recommend them and no greasing is necessary! See affiliate link above).
Wrap one slice of bacon around the inside of each muffin cup and bake for 7-10 minutes (see notes on bacon thickness). Remove from heat and drain the grease. Reposition the bacon in the muffin cup if necessary to make more room for the eggs.
12 slices thick center cut bacon
Crack an egg into the center of each muffin cup, being careful to keep it inside the bacon slice. Sprinkle the top of each egg with salt and pepper, to taste, and bake for 12-15 minutes more depending on the desired amount of doneness (see notes).
12 large eggs, salt and pepper
Remove from the oven and place on a wire rack for 5 minutes. Remove from the muffin cups, serve with chopped fresh chives if desired and enjoy!
1/4 cup chopped chives
Notes
Pro tip: Thick cut bacon takes 10 minutes of cooking time; thin cut bacon takes about 7-8 minutes.
If you like your yolks a bit on the runny side, the eggs should be somewhat "jiggly" on top and baked no more than 12-13 minutes. If you prefer them less runny, bake until set, 14-15 minutes.
Top with grated cheese during the last two minutes of baking if desired.
Store in an air tight container in the refrigerator for up to 5 days and reheat in the microwave for about 40 seconds.
Freeze bacon egg muffins for up to 3 months. Thaw overnight in the refrigerator and heat before serving.