Preheat oven to 375° F. Line muffins tin with paper liners, if desired.
Peel and grate apple to equal 1 1/2 cups.
To almond flour, add coconut flour, honey, eggs, melted butter, cinnamon, nutmeg, vanilla, baking soda, and salt. Mix well until smooth. The mixture will thicken after a few minutes as the coconut flour absorbs liquid.
Stir in coconut flakes, shredded apple, and walnuts if using.
Scoop batter into muffin pan and bake about 20 minutes at 375° F until browned and a toothpick comes out with only a few crumbs.
Either remove muffins from pan to a rack or tilt them in the muffin pan so that the bottoms don't get soggy.