Preheat your oven to 350°F (175°C) and line a standard 12-cup muffin tin with parchment paper liners or silicone cups. Lightly mist the liners with cooking spray.
In a large bowl, whisk together the almond flour, coconut flour, baking soda, salt, cinnamon, and nutmeg. Break up any clumps with your fingers.
In a separate medium bowl, whisk the eggs until slightly frothy (about 30 seconds of whisking). Add maple syrup, melted coconut oil, vanilla extract, and apple cider vinegar. Whisk until smooth and well combined.
Peel and core the apples, then dice into small, uniform 1/4-inch cubes. Pat the apple pieces with a paper towel to remove excess moisture.
Pour the wet ingredients into the dry ingredients and stir gently with a silicone spatula just until combined, about 15-20 folds.
Gently fold in the diced apples, making sure they're evenly distributed throughout the batter. Reserve about 2 tablespoons of apple pieces to sprinkle on top of the muffins before baking.
If using the optional topping, combine coconut sugar, cinnamon, and chopped nuts in a small bowl.
Using an ice cream scoop or 1/4-cup measure, divide the batter evenly among the prepared muffin cups, filling each about 3/4 full. Top with the reserved apple pieces and sprinkle with the cinnamon-sugar mixture if using.
Bake for 22-25 minutes, or until a toothpick inserted in the center comes out clean with just a few moist crumbs. Avoid opening the oven during the first 18 minutes of baking.
Allow muffins to cool in the tin for 5 minutes, then transfer to a wire rack to cool completely.