Preheat oven to 350ºF. Grease muffin cups or line with muffin liners.
Stir together almond flour, coconut flour, oats, salt, baking soda, and baking powder in a mixing bowl. Add in the pumpkin puree, coconut oil, and non-dairy milk. Stir until just moistened. Fold in chopped apple. Fill muffin cups ¾ full.
Add pepitas on top if desired, to garnish, right before baking.
Bake for about 25-28 minutes in the preheated oven, or until a toothpick comes out clean.