Preheat oven to 350°F. Spray a muffin tin with cooking spray and set aside.
Add sausages to a skillet over medium high heat. Stir to crumble sausage. Cook for 4 minutes.
Add onions, green peppers, red peppers and jalapeno to skillet and continue to cook, stirring frequently for an additional 4 minutes or until sausage is cooked and vegetables are softened.
In a large bowl, whisk eggs. Stir in sausage mixture, Armstrong Monterey Jack with Jalapeno cheese and red pepper chili flakes. Season with salt and pepper.
Ladle egg mixture into muffin tin until almost full.
Bake for 15 minutes. Let cool 5 minutes before removing from muffin tin.