Preheat your oven to 350°F (175°C) and line a muffin tin with paper liners or grease them with cooking spray.
In a small bowl, beat the cream cheese with a tablespoon of sugar and a splash of vanilla extract until smooth and creamy. Set aside.
In a large mixing bowl, whisk together the flour, baking soda, baking powder, salt, and pumpkin pie spice until well combined.
In another bowl, beat the eggs, then add the pumpkin puree, vegetable oil, remaining sugar, and vanilla extract. Whisk until all ingredients are well combined.
Gradually add the wet ingredients into the dry ingredients, mixing until just incorporated. Avoid overmixing to keep the muffins light and fluffy.
Spoon a tablespoon of batter into each muffin cup, then add a dollop of the cream cheese filling in the center, and top with more batter until the cups are about two-thirds full.
Place the muffin tin in the preheated oven and bake for about 20-25 minutes or until a toothpick inserted comes out clean.
Remove the muffins from the oven and let them cool in the pan for about 5 minutes, then transfer them to a wire rack to cool completely.