Preheat the oven to 400 degrees F (200 degrees C). Spray a 12-cup muffin tin lightly with cooking spray.
Combine flour, coconut sugar, baking powder, cinnamon, salt, baking soda, nutmeg, allspice, cloves, and ginger in a bowl.
Mix 1 cup plus 2 tablespoons pumpkin puree, applesauce, cashew milk, vanilla extract, and cider vinegar together in a separate bowl. Add mixture to the flour mixture; mix until just combined. Place about 1/4 cup of the mixture into each muffin cup.
Bake in the preheated oven until a toothpick inserted into a muffin comes out clean, 20 to 23 minutes.