Preheat oven to 350 degrees F.
Oil the sides and bottom of a muffin tin.
Soften 12 small, 4" tortillas in the oven or microwave, until soft and flexible, about 25 seconds for 4 tortillas.
Press tortillas into each cup.
Add 1-2 Tablespoons of enchilada sauce into the bottom of each tortilla cup.
Divide 1/2 cup grated cheese between each tortilla cup.
Crack an egg on top of sauce and cheese mixture.
Season with kosher salt and cracked pepper.
Top each egg with 1-2 teaspoons additional enchilada sauce.
Bake in the center of the oven for approximately 20 minutes for a soft egg.
Serve with salsa, sour cream, cilantro and green onions on the side.