Heat the oven to 350°F (175°C). Grease all 12 muffin cups thoroughly with nonstick spray or a little oil, paying special attention to the sides where melted cheese and egg can stick.

Cook the bacon until crisp, drain it on paper towels, and chop it into small pieces. Set aside about 2 tablespoons for sprinkling over the muffins before baking, if desired.

Whisk the eggs, milk or half-and-half, kosher salt, and black pepper in a bowl until the mixture is evenly blended. Do not worry about making it foamy; a smooth mixture is all you need.

Divide the chopped bacon, shredded cheddar, and finely chopped onion among the prepared muffin cups. Distributing the fillings first helps ensure every muffin gets a balanced amount.

Pour the egg mixture into the cups, filling each about two-thirds to three-quarters full. The eggs expand as they bake, so leave room at the top to prevent overflow.

Sprinkle the reserved bacon and a little of the cheese over the tops if desired. Bake for 18–22 minutes, until the centers are set, the tops are lightly puffed, and a knife inserted in the center comes out without liquid egg.

Let the egg muffins rest in the hot pan for 5 minutes after baking. Loosen the edges with a thin knife or small spatula, then lift them out and serve warm.