In a small bowl, mix ground flax seeds and water together and set aside.
In another small bowl, mix together milk and baking soda. Set aside.
In a large mixing bowl, whisk wet ingredients together (applesauce, oil, pumpkin puree, sugar and vanilla). Stir in flax egg and milk mixture.
Add dry ingredients (spices, baking powder, salt, flours) and mix into wet ingredients with a wooden spoon. Add chocolate chips.
Divide the dough into 12 cookies using a tablespoon or an ice cream scoop. Place on a baking sheet lined with a silicon mat and bake in the oven for 12 to 15 minutes.
Let cool one minute before transferring to a cooling rack.