Preheat oven to 375F. Heat a large skillet to medium and fry the bacon until crisp. Remove the bacon from the pan, allow to cool and set aside.
In the same skillet 1 tablespoon of the bacon grease, add in the jalapeño peppers and onions. Sauté for a few minutes, until softened slightly. Then drain, cool and combine with the bacon and shredded pepper jack cheese in a small bowl.
In a large mixing bowl, add in the eggs, cream cheese, smoked paprika, salt and pepper and mix using a hand mixer. The cream cheese will not fully combine, so you will have little chunks, and that’s ok! This will give you little cream cheese chunks when you bite into the egg cups.
Using a silicone muffin pan or muffin pan sprayed with nonstick spray, add in the bacon mixture into the muffin pan making sure it’s evenly distributed. Pour the egg mixture over the tops and bake for 15-18 minutes or until the eggs have set. Store leftovers in an airtight container for a few days or freeze.