Preheat the oven to 375°F. Generously spray a 12-cup muffin tin with nonstick cooking spray.
In a large skillet over medium-high heat, cook the breakfast sausage, breaking it into small crumbles, for 6 to 8 minutes or until browned and no pink remains. Drain excess fat.
Add the diced onion and bell pepper to the skillet with the sausage and cook for 3 to 4 minutes, until the veggies soften. Remove from the heat and let the mixture cool slightly.
In a large mixing bowl, whisk together the eggs, milk, salt, black pepper, garlic powder, onion powder, smoked paprika (if using), and chopped parsley or chives until well combined.
Stir the cooked sausage and vegetable mixture into the egg mixture. Fold in the shredded cheddar and mozzarella (or Monterey Jack) cheese until evenly distributed.
Divide the mixture evenly among the 12 prepared muffin cups, filling each almost to the top.
Bake for 18 to 22 minutes, or until the muffins are set, lightly golden on top, and a toothpick inserted in the center comes out clean.
Let the muffins cool in the pan for about 5 minutes, then run a thin knife around the edges to loosen and carefully remove them. Serve warm or cool completely for storing.