Preheat oven to 350°F. Place a 12-cup silicone miniature-muffin tin on a large rimmed baking sheet.
Cook bacon in a large skillet over medium heat, turning occasionally, until crisp, 8 to 10 minutes. Transfer to a plate lined with paper towels to cool, about 5 minutes. Crumble into small pieces.
Whisk together eggs, salt, and pepper in a large bowl until combined. Stir in half the cheese. Divide bacon pieces evenly among the muffin cups, and spoon egg mixture over bacon, filling cups to the top. Top with remaining cheese. Bake until puffed and just golden, 15 to 18 minutes.