Preheat your oven to 375°F (190°C). Grease a muffin tin with cooking spray or olive oil to prevent sticking.
Heat olive oil in a skillet over medium heat. Add diced bell peppers and onions to the skillet and sauté until they are soft and lightly caramelized, about 5-7 minutes. Season with salt and pepper to taste. Set aside to cool slightly.
In a mixing bowl, crack the eggs and beat them until well combined. Add the whole milk.
Add the breakfast sausage to the beaten eggs and mix until evenly distributed. The sausage will add extra protein to the egg cups.
Once the sautéed peppers and onions have cooled slightly, add them to the egg mixture and stir until combined.
Spoon the egg mixture evenly into the greased muffin tin, filling each cup about three-quarters full. If desired, sprinkle shredded cheese on top of each egg cup for extra flavor.
Place the muffin tin in the preheated oven and bake for 20-25 minutes, or until the egg cups are set and lightly golden on top.
Remove the muffin tin from the oven and allow the egg cups to cool for a few minutes before carefully removing them from the tin.