Preheat the oven to 350°F (175°C). Coat the cups of a standard 12-cup muffin pan thoroughly with nonstick cooking spray, including the upper edges where the eggs may rise.

Place the breakfast sausage in a 10-inch skillet over medium heat. Cook for 5 to 7 minutes, breaking it into small crumbles with a spoon. Continue until no pink remains and the sausage reaches 160°F (71°C).

If more than a thin coating of grease remains in the skillet, carefully spoon it out. Excess fat can settle at the bottom of the muffin cups and make the eggs feel oily.

Add the diced onion and bell pepper to the cooked sausage. Cook over medium heat for 3 to 4 minutes, stirring occasionally, until the onion begins to look translucent and the pepper softens slightly. Remove the skillet from the heat.

Crack the eggs into a large mixing bowl: Add the milk, salt, and black pepper. Whisk until the yolks and whites are completely blended and the mixture looks evenly pale yellow.

Stir 3/4 cup (85 g) of the shredded cheddar into the egg mixture. Reserve the remaining 1/4 cup (30 g) for topping.

Spoon the sausage and vegetable mixture evenly among the 12 prepared muffin cups. Each cup should contain approximately 2 tablespoons of filling.

Pour or ladle the egg mixture evenly into the muffin cups, filling each about three-quarters full. Stir each cup gently with the tip of a spoon so the sausage and cheese are distributed rather than sitting only at the bottom.

Sprinkle the reserved cheddar evenly over the muffin cups. Keep the cheese mostly inside the edges of each cup to reduce sticking.

Bake on the center rack for 18 to 21 minutes. The muffins are done when the tops look set, the edges are lightly golden, and the centers no longer ripple when the pan is gently moved. The center of an egg muffin should reach 160°F (71°C).

Place the pan on a wire rack and let the muffins cool for 5 minutes. They may puff in the oven and settle slightly as they cool; this is normal.

Run a thin silicone spatula or butter knife around the edges, then lift the muffins from the pan. Garnish with sliced green onions, if using, and serve warm.