Preheat the oven to 350ºF. Line a 12 cup muffin tin with parchment paper cups or silicone baking cups to keep the muffins from sticking.
In a large bowl, combine the wet ingredients (eggs, milk, melted ghee, honey, and apple cider vinegar) until smooth.
In a separate bowl, mix the dry ingredients (almond flour, coconut flour, baking powder, baking soda, and salt).
Add the dry ingredients to the wet slowly until fully incorporated and smooth.
Distribute the batter evenly into the muffin tin (I added 6 standing silicone muffins cups to a baking sheet to make 18 total muffins). Transfer to the preheated oven, and bake for 20 to 25 minutes or until muffins are golden brown on top and a toothpick comes out clean.