Preheat your oven to 400 degrees F and line a muffin tin with cupcake liners.
In a large bowl, whisk together your gluten-free flour, baking soda, nutmeg, pumpkin pie spice, cinnamon, and salt.
In another bowl, mix your pumpkin puree, granulated sugar, vegetable oil, eggs, vanilla extract, and water until smooth. Now, fold the dry ingredients into the wet until combined. Let muffin batter sit for 15 minutes.
In a small bowl, mix together the cream cheese and granulated sugar using a hand mixer. Then add in flour and vanilla until creamy. Add to a piping bag with a round tip.
Fill your muffin cups a little over 3/4 of the way full with the pumpkin batter. Then stick your piping bag half way down each muffin and pipe the cream cheese icing, pulling up while pressing the cream cheese into the batter.
Sprinkle each muffin with pumpkin seeds for the full Starbucks effect.
Pop those muffins in the oven for 10 minutes. Then turn down oven to 350 degrees F and bake for another 13-18 minutes, or until a toothpick comes out clean from the pumpkin part (avoid the cream cheese!). Let them cool for 10 minutes in muffin tray before diving in—if you can wait that long.