Preheat the oven to 350 degrees F. Line two muffin tins with cupcake liners. Set them aside.
In a medium-sized bowl, whisk together the flour, baking soda, baking powder, cinnamon, nutmeg, cloves, and salt. Set aside.
In the bowl of a stand mixer, beat together the pumpkin puree, sugars, vegetable oil, and milk. Add the eggs, one at a time, until well combined.
Little by little, add the dry ingredients to the wet, mixing until everything is just combined. Fill the cupcake liners about ¾ of the way full. Bake for 18-20 minutes or until a toothpick, when inserted into the center of the cupcakes, comes out clean. Allow them to cool for a few minutes in the tin, then remove them to a wire rack to finish cooling completely.