Prepare the Cream Cheese Swirl:
In a small bowl, mix softened cream cheese and sugar until smooth. Set aside.
Mix Dry Ingredients:
In a large bowl, whisk together brown rice flour, sorghum flour, tapioca starch, cinnamon, baking soda, xanthan gum, ginger, nutmeg, salt, and cloves.
Mix Wet Ingredients:
In another bowl, whisk eggs, brown sugar, white sugar, pumpkin puree, oil, applesauce, and vanilla extract until combined.
Combine Wet & Dry Mixtures:
Pour the wet ingredients into the dry mixture and fold gently until just combined. Do not overmix.
Assemble the Muffins:
Preheat oven to 350°F (175°C) and line or grease a muffin tin.
Fill each cup ¾ full with batter. Add 1 tsp cream cheese mixture on top and gently swirl with a toothpick.
Optionally, sprinkle pumpkin seeds or chopped nuts on top.
Bake:
Bake for 20–25 minutes, or until a toothpick inserted into the muffin (avoiding the cream cheese) comes out clean.
Cool & Serve:
Let muffins cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.