Preheat the oven to 200º Celsius (400º Fahrenheit) and line a muffin tray with muffin liners
Add the chopped bacon to a skillet on medium heat and cook for 6-8 minutes until the bacon is crisp. Set the bacon aside on a plate and leave one tablespoon of the bacon grease in the pan. Add in the chopped onion and shaved brussels sprouts, season with salt and pepper and saute for 5 minutes until the brussels sprouts begin to soften.
While the brussels sprouts are cooking, crack the eggs into a large bowl and whisk together with the almond milk. Add in the dijon mustard, apple cider vinegar, baking soda and coconut flour and stir. Finally add the cooked bacon and shaved brussels sprouts and sauteed onion to the batter and stir until combined. Divide the batter between 10-12 muffin cups ensuring that you fill them right to the top.
Bake in the oven for 25 minutes until the muffins are golden in colour and the tops are completely dry. Allow them to cool for 10 minutes in the tray on the countertop before removing and transfering to a wire rack. Store the muffins in an airtight container in the fridge.