Heat oven to 350°F. Line a baking sheet with parchment paper and set aside.
Add almond flour, coconut flour, ground cinnamon, baking soda, baking powder, and sea salt to a medium-sized mixing bowl. Whisk together until ingredients are incorporated and no lumps remain.
Add canned pumpkin, honey, coconut oil, egg, and vanilla extract to a large mixing bowl and stir until combined. Slowly add the dry ingredients, mixing with a silicone spatula, until no dry spots of flour remain. The dough will be thick. Stir in ½ cup of chocolate morsels.
Form dough into balls using a 3 tablespoon cookie scoop. Flatten each ball into a ½ inch tall circle using your hands. Place cookies 1 inch apart on the parchment-lined baking sheets. Add the remaining ¼ cup of chocolate morsels on top of the cookies.
Bake for 17 - 20 minutes until the cookies are slightly browned. Allow cookies to cool on the baking sheet for 10 minutes, then transfer to a wire rack to completely cool.
Store in an airtight container at room temperature for up to 5 days.