Preheat oven to 425 degrees F and line a muffin tin with 15 paper liners.
In a medium mixing bowl, mix flour, baking soda, salt, cinnamon, and nutmeg.
In a large mixing bowl, whisk eggs, pumpkin, sugars, oil, and milk together. Add the dry mix and whisk until combined.
Fill each liner with 2 tablespoons of the batter and place 1/2 teaspoon in the middle. Swirl with a toothpick and then top with about 1 1/2 tablespoons more batter. Add another 1/2 teaspoon to the top and swirl again.
Bake for 5 minutes and then lower temperature to 350 degrees and bake 15-16 more minutes.
Leave muffins in tins for 5 minutes before removing from pan.