Preheat oven to 375 degrees.
In a large glass mixing bowl, combine eggs and milk and whisk well.
Stir in 3/4 c. cheese, cooked bacon, salt, and pepper.
Divide mixture evenly among 12 greased muffin cups.
Sprinkle with remaining 1/4 c. cheese and fresh chives.
Bake at 375 degrees for 20 minutes or until centers are set and muffins are beginning to brown.