Preheat the oven to 350 degrees F (175 degrees C). Line a muffin pan with paper liners.
Combine bacon, onion, and green bell pepper in a medium mixing bowl. Divide bacon mixture among the muffin cups, filling each 3/4 full. Crack 1 egg into each cup. Sprinkle chives and a pinch of salt over each egg.
Bake in the preheated oven until eggs are set, about 20 minutes.