Preheat oven to 350°F and lightly coat a muffin tin with nonstick cooking spray. Cut 12, 4-inch rounds out of rolled out pie crust. Press dough into each muffin cup, pricking dough several times with a fork. Bake pie dough for 7 to 10 minutes. Remove from oven and set aside until cool enough to handle.
Press a slice of cheese into each cup and sprinkle with crumbled bacon. Carefully break an egg into each cup and season with salt and pepper. Transfer to oven and bake for 20 minutes, or until egg whites are set.
Garnish with chopped chives and serve immediately.