Preheat oven to 350. Line 12 cup muffin pan with cupcake liners and generously spray the inside of each liner with nonstick cooking spray.
Add peanut butter, avocado oil, coconut sugar and vanilla to the bowl of an electric mixer and mix on medium speed until well combined. Slowly add in eggs, one at a time; beat again for one minute until batter is smooth and creamy. Pour in almond milk and mix on low speed until combined.
In a small bowl whisk together coconut flour, baking powder, and raw cacao powder. Slowly add dry ingredients to wet ingredients and mix on low speed until batter is smooth and creamy. Fold in chocolate chips with a wooden spoon.
Fill each muffin cup 2/3 full. Bake for 18-20 minutes or until a toothpick comes out clean with a few crumbs attached. Cool for 5 minutes then immediately transfer to a wire rack to finish cooling.