Preheat the oven to 350 degrees F (175 degrees C). Lightly grease a 12-cup muffin tin.

Cook sausage in a large skillet over medium-high heat until browned and crumbly, 5 to 7 minutes. Drain.

Combine eggs, onion, and chile peppers in a large bowl. Add sausage, salt, and pepper; mix until well combined. Spoon 1/4 cup sausage mixture into each of the prepared muffin cups.

Bake in the preheated oven until eggs are set and a toothpick inserted into the center comes out clean, 15 to 20 minutes.