Preheat your oven to 400°F (200°C). Line a 12-cup muffin pan with paper liners.
In a large bowl, mix together the all-purpose flour, granulated sugar, brown sugar, baking powder, baking soda, salt, cinnamon, nutmeg, and ginger.
In a separate bowl, beat the eggs. Stir in the oil, vanilla extract, and pumpkin puree.
Pour the wet mixture into the dry ingredients. Stir until just combined; do not overmix.
In a small bowl, combine the softened cream cheese and powdered sugar. Mix until smooth and creamy.
Fill each muffin cup halfway with the pumpkin batter. Add a spoonful of the creamy cream cheese filling to the center of each. Top with more pumpkin batter, filling each cup about two-thirds full.
Sprinkle the tops of the muffins with crunchy pumpkin seeds.
Bake for 18-22 minutes, or until a toothpick inserted into a muffin comes out clean.
Let the muffins cool in the pan for a few minutes. Then transfer them to a wire rack to cool completely.