Preheat the oven to 400 degrees.
Add the pumpkin puree, eggs, sugar, and applesauce to the mixing bowl. Using a whisk, mix the ingredients together.
To get the smoothest batter, place a mesh strainer over the mixing bowl. Add the flour, baking soda, baking powder, salt, and cinnamon to the strainer. Gently tap the side of the strainer until all the ingredients have sifted through and fallen into the bowl.
Mix the ingredients together until the batter is smooth.
Add the chocolate chips to the batter. Mix the chocolate chips in until they are throughout the batter.
Place muffin/cupcake liners in each hole of the muffin pan.
Use a spoon or a scoop to fill the muffin liners 3/4 full.
Optional - Place a few chocolate chips on top of the batter. This ensures chocolate chips are visible on top when the muffin is done baking.
Bake for 18-20 minutes. To check for doneness, place a toothpick in the center of one of the muffins. If the toothpick comes out clean then the muffins are done. Note: the toothpick may have melted chocolate on it but it shouldn't have any batter on it.
Place the pan on a cooling rack. Allow the muffins to cool for 10 minutes in the pan and then remove them.