Brown sausage with diced bell peppers and onion over medium-high heat, until no longer pink in large skillet.
In medium bowl, whisk together eggs, milk and black pepper.
Using a cookie or biscuit cutter, cut 3 ½-inch circles from whole-wheat tortillas until you have 12 circle cutouts. Set tortilla scraps to the side.*
Spray muffin tin with non-stick cooking spray.
Press a tortilla circle into each muffin cup using your fingers.
Spoon 1 tablespoon of the sausage-vegetable mixture into each tortilla cup.
Sprinkle each tortilla cup with approximately 2 teaspoons of shredded cheese.
Pour egg mixture into each tortilla cup until the egg mixture just barely reaches the top of the tortilla.
Bake for 15-20 minutes, until egg mixture has set.
Allow tortilla cups to set for 5 minutes before serving. Serve warm.
Refrigerate any leftovers and reheat in the microwave for approximately 30 seconds.
*Note
For a sweet treat, place tortilla scraps onto baking sheet. Spray tortillas with non-stick cooking spray and sprinkle with cinnamon sugar. Flip tortilla scraps over and repeat. Bake at 350°F until golden brown.