Coat 12 standard-size muffin cups with cooking spray. Divide broccoli and bacon evenly among muffin cups.
Crack eggs into a large bowl. Add milk, salt, and pepper; stir with a whisk until well combined. Divide egg mixture evenly among muffin cups. Sprinkle cheese evenly on top. Bake at 350°F for 18 to 20 minutes or until just set. Cool on a wire rack for 2 to 3 minutes; run a thin knife around edge of each frittata to release from pan. Remove frittatas from pan.