Preheat the oven to 350°F. Line a muffin tin with cupcake liners.
In a large bowl or stand mixer, mix the almond flour, coconut sugar, coconut flour, tapioca flour, baking powder, baking soda, and salt. Stir to blend.
In the medium mixing bowl beat together the eggs, dairy-free milk, applesauce, coconut nectar or maple syrup, and vanilla extract. Whisk until creamy.
Pour the wet ingredients into the bowl with the flour mixture. Beat until a batter is formed, increasing the speed as needed.
Transfer the batter into the cupcake liners, filling the cups about two-thirds to three-quarters of the way full. Bake for 22 to 24 minutes, until the tops are golden brown and a toothpick inserted into the center of one comes out clean. Allow the cupcakes to slightly cool for 5 to 10 minutes in the muffin tin, before transferring them to a wire rack to cool completely before frosting, about 1-2 hours.
Make the frosting. In a large bowl, combine the coconut oil and grass-fed butter. Beat with a hand mixer until fluffy, about 30 seconds. You can also use a whisk to beat by hand.
Add the remaining ingredients and beat again, using a spatula to scrape down the sides as needed.
Using a spatula, mix the frosting. Frost the cooled cupcakes immediately, or transfer the frosting to the refrigerator for 10 minutes for a denser texture.