Preheat oven to 350°F and generously spray a 12-cup muffin tin with cooking spray.
Cut tortillas into circles that fit your muffin tin (about 3.5 inches). Press each tortilla circle into the muffin cups.
In a large bowl, whisk together eggs and milk until well combined.
Stir in the cooked taco meat, half the cheese, and salsa.
Pour the egg mixture evenly into tortilla cups, filling about 3/4 full.
Sprinkle remaining cheese on top.
Bake for 15-18 minutes for mini muffin tins, or 26-28 minutes for regular-sized muffin tins, until eggs are set.