Preheat the oven to 350°F (177°C). Grease a 12-cup muffin pan. ( I like to spray mine with olive oil spray). Set aside.
Whisk the almond flour, tapioca flour, coconut flour, cocoa powder, baking soda, and salt together in a large bowl until combined.
In a medium bowl, whisk the eggs, coconut sugar, olive oil, and vanilla together until smooth. Pour half of the wet ingredients into the dry ingredients. Then add half of the almond milk on top of that. Whisk for a few seconds, then add the remaining wet ingredients and almond milk. Whisk until combined; do not overmix. Stir in the chocolate chips.
Evenly pour the batter into the muffin tins. Bake for 18-20 minutes, or until a toothpick comes out clean.