Preheat the oven to 350°F. Line two baking sheets with parchment paper and set aside.
In a large bowl, add the melted and cooled ghee, egg and egg yolk, coconut sugar, and vanilla extract. Whisk to combine for 30 seconds until smooth. Set aside.
In a separate bowl, add the almond flour, oats, salt, baking powder, baking soda, cinnamon, and nutmeg. Whisk to combine until all the dry ingredients are totally combined.
Add the dry ingredients to the wet ingredients and stir to combine using a wooden spoon. Mix for one minute to allow the oats to soak up some of the liquid.
Add in the apples and mix until just combined. Cover the bowl with cling wrap and transfer to the fridge. Chill for 30 minutes.
Remove from the fridge. Using a large cookie scoop, portion into 12-14 large cookies. Roll into balls and place 6 cookies on each sheet, spacing at least 2 inches apart. If any of the apples fall out while forming the cookie, press them into the cookie tops. Gently press the tops down slightly using a spatula.
Bake for 13-15 minutes, rotating the baking sheets halfway through if baking both trays at once. The cookies are ready when the tops are golden and the edges are crisp.
Allow the cookies to cool on the baking sheets. For perfectly round cookies, immediately place a glass with an opening slightly larger than each warm cookie around it and gently move the glass in a circular motion. Let the cookies cool completely before glazing.