Preheat oven to 350 degrees F (175 degrees C). Prepare 12 muffin cups with cooking spray.
Cook bacon in a large skillet over medium-high heat, turning occasionally, until evenly browned but not yet crispy, 7 to 10 minutes. Drain the bacon slices on paper towels.
Line the walls of each muffin cup with a bacon strip.
Beat eggs with salt and pepper in a large bowl; ladle into muffin cups to about 3/4-full. Sprinkle cheddar cheese over the top of each portion.
Bake in preheated oven until golden brown on top and the egg doesn't jiggle, 20 to 35 minutes. Remove from oven and use a butter knife or spoon to remove from muffin tin promptly so that they don't stick.