Preheat & Prep. To start, preheat oven temperature to 425 degrees F. Line a muffin pan with parchment paper liners and set aside.
Make Streusel. In a small mixing bowl, combine gluten-free flour, brown sugar, cinnamon, and melted butter. Stir with a fork until all the dry ingredients are coated in butter and clusters form.
Start Dry Ingredients For Muffin Batter. In a large mixing bowl, combine gluten-free flour, baking powder, baking soda, cinnamon, nutmeg, ginger, cloves, and salt. Whisk until well blended.
Add Wet Ingredients. Then, add pumpkin puree, oil, milk, brown sugar, sugar, eggs, and vanilla. Whisk to combine until muffin batter is smooth.
Make Cream Cheese Filling. In a medium bowl, combine softened cream cheese, 3 Tablespoons sugar, egg yolk, and 1 teaspoon vanilla. Beat with a hand mixer on medium speed 1-2 minutes until smooth and fluffy. (You *can* mix this by hand, just make sure the cream cheese is soft before starting!)
Layer Muffins. Use a medium cookie scoop to add 1 1/2 Tablespoons muffin batter into each muffin cup. Then, use a small cookie scoop to add 1 Tablespoon cream cheese filling to the center of each muffin cup. I like to slightly flatten the cream cheese out a bit so it doesn't sink later. Then, top with another scoop (1 1/2 Tablespoons) of pumpkin batter on top of the cream cheese layer. Add about a 1 Tablespoon scoop of streusel topping on top of each muffin, lightly pressing it into the batter so it doesn't fall off during baking.
Bake & Cool. Now, bake the muffins for 5 minutes at 425 degrees, then (leaving the muffins in the oven), reduce the oven temperature to 350 degrees and bake another 15-18 minutes, or until muffins are fully baked. Let muffins cool 2-3 minutes in the pan, then transfer to a wire rack to finish cooling before eating.
Serve & Store. Enjoy cooled muffins right away. Store leftover muffins in an airtight container 2-3 days in the fridge, for best results, or freeze in a freezer-safe ziplock bag for up to 2 months!