Step 1: Preheat and Prep. Preheat your oven to 375°F (190°C). Line a 12-cup muffin tin with paper liners or lightly grease with non-stick cooking spray to ensure the muffins release easily after baking.
Step 2: Prepare the Cream Cheese Filling. In a medium bowl, beat the softened cream cheese and powdered sugar together until the mixture is smooth and creamy. Use a hand mixer for the best results to ensure there are no lumps.
Step 3: Combine Dry Ingredients. In a large mixing bowl, whisk together the flour, pumpkin pie spice, baking soda, and salt. Make sure the spices are evenly distributed through the flour mixture.
Step 4: Mix Wet Ingredients. In a separate bowl, whisk together the pumpkin puree, granulated sugar, brown sugar, eggs, oil, and vanilla extract until well combined and smooth.
Step 5: Fold the Batter. Gently fold the wet ingredients into the dry ingredients. Use a spatula and mix only until just combined. Be careful not to overmix, as this can make the muffins tough.
Step 6: Assemble the Muffins. Fill each muffin cup about half full with the pumpkin batter. Place a generous tablespoon of the cream cheese mixture into the center of each cup. Top with the remaining pumpkin batter to cover the cream cheese. If desired, sprinkle a few pepitas on top.
Step 7: Bake and Cool. Bake for 18 to 22 minutes, or until a toothpick inserted into the cake part (avoiding the cream cheese center) comes out clean. Allow the muffins to cool in the pan for 5 minutes before transferring them to a wire rack to cool completely.