Preheat the oven to 350ºF. Line 12 cups of a standard muffin pan with paper liners.
In a large bowl, whisk together the coconut flour, baking soda, and salt. In a medium bowl, whisk together the eggs, coconut oil, coconut sugar, and lime zest. Pour the wet ingredients over the dry and whisk quickly to form a thick and uniform batter. Divide the batter evenly between the lined muffin cups.
Bake for 15-20 minutes until golden brown and a toothpick inserted comes out clean. Cool the cupcakes for 5 minutes in the pan then transfer to a wire rack to cool completely.
In a small pot set over low heat, combine the coconut butter, milk, and stevia. Whisk constantly until melted, thick, and smooth. Spread over the cooled cupcakes and top with coconut flakes. Serve.