Preheat oven to 350. Line cupcake tray with liners and spray them with cooking spray to help the muffin batter not adhere to them during baking.
Add the flours, pumpkin pie spice, granulated sugar free sweetener, and baking soda in a bowl and stir to combine.
Stir in the pumpkin puree, vanilla, eggs, and melted butter. Mix thoroughly with a wooden spoon until the it becomes a thick batter.
Add about 1/4 cup rounded of batter to each of the 12 muffin cups. Press down in the center with a large spoon or the rounded end of a pestle to create a hollow depression for the cream cheese mixture.
Mix the cream cheese, sugar-free icing sugar, and whipping cream with a hand mixer or mix-master until thoroughly blended and smooth.
Spoon the cream cheese mixture evenly between the muffins.
Top with the pumpkins seeds and bake for 20-25 minutes until fully cooked and lightly browned.