Preheat the oven to 375°F (190°C) and grease muffin pans with cooking spray. Swirl the spray around each muffin well using a paper towel to make sure the grease is evenly distributed and to dab off any excess.
In a medium bowl, whisk together the flour, baking powder, baking soda, salt and spices.
In a large bowl, whisk together the eggs, applesauce and sugar until completely combined. Then whisk in the pumpkin, water and vanilla. Whisk in half of the flour mixture until just combined, and then whisk in the rest. Be careful not to over mix! Fold in the chocolate and cinnamon chips.
Fill each muffin cup 3/4 full. Fill any empty muffin cups 3/4 full of water for more even baking. Bake for 15-18 minutes, or until the edges are lightly browned. Let the muffins rest in the pans for 5 minutes before removing to a wire cooling rack. Store in an airtight container and enjoy!