Prepare muffin tin by spraying with nonstick spray or lining with cupcake liners.
In a medium bowl, combine flours, baking powder, baking soda, salt, cinnamon, ginger, and nutmeg. Whisk together until combined.
In a large bowl, whisk together pumpkin, eggs, oil, sugar, and milk until the mixture is smooth. Add in the dry ingredients and mix well.
Divide the batter evenly among the prepared muffin tins. Bake for 20 to 25 minutes, or until the tops of the muffins are puffed and spring back slightly when pressed or when a toothpick is inserted it comes out clean.