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Preheat oven to 350 degrees. In a sauté pan, heat olive oil. Add onion and cook for about 2 minutes. Add spinach and cook until wilted, about 2-3 more minutes. Add the minced garlic and cook for 30 seconds. Sprinkle with a little salt and pepper. Remove from the heat.
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In a bowl, whisk together the eggs, milk, and the cheese. Season with the salt and pepper. Add the spinach mixture and the bacon and stir until well-combined.
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Either use a silicone muffin pan or spray 24 mini muffin tin with non-stick spray. Evenly distribute the egg mixture amongst each muffin tin (I filled mine about ¾ of the way). Bake for about 15 minutes or until the muffins have turned a light golden brown around the edges (20 minutes if you use large muffin pans).
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Store leftover muffins in the fridge in an airtight container. To reheat, stick in the microwave for about 15-20 seconds.