Preheat oven to 350 degrees F. Spray 12-cup muffin tin with nonstick spray.
In a large bowl, whisk together the eggs, milk,salt & pepper. Equally divide ham and 1/2 cup of cheese between the muffin cups. Reserve the extra 2 tablespoons of cheese for later.
Pour egg mixture on top of the cheese and ham, so that muffin cups are a little more than 1/2 full. (They will rise like a souffle as they bake, then deflate when you pull them out of the oven.)
Bake for about 20 minutes until eggs are set, then remove from oven. Sprinkle remaining 2 tablespoons of cheese over the muffins, then bake for a few minutes longer until cheese is melted.
Sprinkle with chives and serve warm, using a butter knife to remove the muffins from the cups.