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Grease and flour a 12 cup muffin pan.
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Peel and dice the shallots
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Trim and chop the scallions into rings
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Place a layer of paper towels next to the stove.
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Place the bacon in a skillet and cook until crispy.
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Transfer to the paper towels and let drain.
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Add the shallots and scallions to the bacon fat and cook, stirring, until soft. Remove from heat.
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Transfer the shallots and scallions to a bowl. Use a slotted spoon if there is an excess of bacon grease.
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Chop the bacon into pieces and add it to the bowl.
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In a separate bowl. Whisk together the flour, baking powder, and salt.
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Add the dry ingredients, half the shredded cheese, chives, to the fried ingredients and mix.
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Mix in the sour cream, 1 egg, oil, and the buttermilk.
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Add a few turns of freshly ground pepper.
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Preheat the oven to 350 degrees F.
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Spoon the batter into the prepared pans. Use your fingers (wet them first) to gently press the batter into the pan and about 1/4 inch up the sides, forming a cup.
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Crack one egg into each of the wells.
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Gently arrange enough batter over the eggs, covering them but making sure not to break the yolks.
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Sprinkle the rest of the cheese over the tops.
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Place in the oven and bake for 30 minutes.
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Remove from oven and let stand for 15 minutes in the pan before removing and serving.