Preheat the oven to 350°F and line 9 muffin tins with parchment paper liners or silicone liners.
In a bowl, whisk together the almond flour, coconut flour, baking powder, baking soda, and salt until well blended.
Add the eggs, honey, applesauce, and vanilla extract and mix until smooth.
Pour into the lined muffin cups, filling each about 1/2 full, and bake for 15 to 20 minutes, or until a toothpick inserted in the middle comes out clean.
While cupcakes cool, make the frosting: In a stand mixer fitted with a whisk attachment or using a hand mixer, mix the butter for 1 minute. Add the powdered sugar and mix on low speed until well blended, then increase the speed to medium and beat until fluffy, about another 3 to 5 minutes. Add the vanilla, and almond milk. Continue to beat on medium speed for 1 minute, adding an additional tablespoon of almond milk, or more, if needed for a soft consistency.
Apply the frosting in a mound on the cupcake with a spatula or using a piping bag fitted with a circle piping tip.
Cut the marshmallows in half on a diagonal. Dip the cut side in the colored sugar. Place each ear on top of the buttercream frosting, pushing in slightly to adhere. Sprinkle the flaked coconut on top of the buttercream frosting.
Cupcakes will keep in the refrigerator for up to 3 days.