Preheat oven to 400˚F. Generously coat 18 standard muffin cups with cooking spray.
In a medium bowl, combine the almond flour, whole wheat flour, baking powder, baking soda, salt, cinnamon, ginger, nutmeg, and cloves, using a whisk.
In a large bowl, whisk the eggs, pumpkin, honey, oil, and vanilla until well combined.
Add the flour mixture to the pumpkin mixture and combine, using a wooden spoon, until thoroughly blended. Gently fold in the apples.
Divide the batter evenly among the 18 muffin cups.
Bake for 13 to 16 minutes, or until a toothpick inserted into the center of a muffin comes out clean. Remove muffins from pan and cool on a wire rack.