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.
Transfer to the oven and bake for 7 minutes. Remove from the oven, gently press the tops down slightly again, and rotate the trays to ensure the tray that was on the lower rack is now on the upper rack and vice versa. Bake for an additional 7 to 8 minutes, or until the tops are golden and the sides are crisp.
Remove from the oven. This is totally optional but will make the cookies perfectly uniform: using a glass with an opening slightly larger than the cookies, place the glass around each cookie, and gently wiggle the glass back and forth a bit to get perfectly round edges. Allow to cool completely.