Step 1: Preparation. Preheat your oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or grease them lightly with cooking spray to ensure the muffins don’t stick.
Step 2: Mixing Dry Ingredients. In a large mixing bowl, whisk together the flour, 1 cup of sugar, brown sugar, baking soda, salt, and pumpkin pie spice until well combined and no lumps remain.
Step 3: Combining Wet Ingredients. In a separate medium bowl, whisk the two eggs, pumpkin puree, oil, and 1 teaspoon of vanilla extract until the mixture is smooth and uniform.
Step 4: Making the Batter. Gently fold the wet ingredients into the dry ingredients using a spatula. Mix just until combined; be careful not to overmix, as this can make the muffins tough.
Step 5: Preparing the Filling. In a small bowl, beat the softened cream cheese, ¼ cup of sugar, egg yolk, and remaining vanilla extract together until the mixture is creamy and smooth.
Step 6: Layering the Muffins. Add about 1.5 to 2 tablespoons of pumpkin batter into each muffin liner. Place 1 rounded tablespoon of the cream cheese mixture in the center, then top with another 1 tablespoon of pumpkin batter to cover the filling.
Step 7: Baking and Cooling. Bake for 22 to 25 minutes, or until a toothpick inserted into the pumpkin part of the muffin comes out clean. Allow them to cool in the pan for 10 minutes before transferring them to a wire rack.