Preheat oven to 350°F (175°C). Grease a 12-cup muffin tin with cooking spray or olive oil.
Cook breakfast sausage in a skillet over medium heat until browned; drain excess fat and set aside.
In the same skillet, sauté shallots until translucent. Add spinach and cook until just wilted. Remove excess moisture by squeezing spinach in a strainer or with paper towels.
In a blender, combine eggs, cottage cheese, salt, and pepper. Blend until smooth.
evenly distribute the sausage, sautéed shallots and spinach, and fire-roasted red bell pepper into the muffin cups.
Pour the egg and cottage cheese mixture over the fillings in each muffin cup until nearly full.
Sprinkle shredded cheese over the top of each cup.
Bake for 25-30 minutes or until egg bites are set and lightly golden on top.
Let cool for 10 minutes before removing from the muffin tin. Serve warm or store in an airtight container in the fridge for up to 5 days or freeze for longer storage.