Preheat the oven to 375 degrees F (190 degrees C). Coat a 6-cup muffin pan with cooking spray.
Beat eggs and sour cream together until frothy in a bowl. Fold in cheese, onion, and bacon. Season with cayenne, salt, and pepper.
On a clean work surface, cut out 4 circles from the flour tortilla using the rim of a heavy glass or a cookie cutter. Lay 1 circle in each of 4 muffin cups. Gently press the tortilla to fit snugly to the sides of the cup.
Pour egg mixture into each muffin cup. Sprinkle lightly with more cheese.
Bake in the preheated oven for 15 minutes, then check for doneness - a toothpick inserted in the middle should come out clean. Let the pan sit for about 5 minutes, then remove the entire cup to serve.