Prepare the Oven and Muffin Pan: 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. This ensures that the muffins release easily after baking.

Brown the Sausage: 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). This step is crucial for flavor and safety.

Drain Excess Fat: 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. Proper drainage helps maintain the muffins' texture.

Cook the Vegetables: 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. This step enhances the flavor and texture of the muffins.

Whisk the Egg Mixture: 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. This ensures a uniform texture throughout the muffins.

Add the Cheese: Stir 3/4 cup (85 g) of the shredded cheddar into the egg mixture. Reserve the remaining 1/4 cup (30 g) for topping. The cheese adds flavor and helps bind the muffins together.

Divide the Sausage Mixture: Spoon the sausage and vegetable mixture evenly among the 12 prepared muffin cups. Each cup should contain approximately 2 tablespoons of filling. This ensures even distribution of flavors in every muffin.

Add the Eggs: 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. This step is important for even cooking.

Top with Cheese: Sprinkle the reserved cheddar evenly over the muffin cups. Keep the cheese mostly inside the edges of each cup to reduce sticking. This adds a delicious cheesy crust on top.

Bake the Muffins: 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) for safe consumption.

Cool Briefly: 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. Allowing them to rest helps them firm up for easier removal.

Remove and Serve: 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. This final touch adds freshness and color to the dish.