Preheat the oven to 425°F (220°C), or 200°C for a fan oven. Line a 12 count muffin tin with paper liners and set aside
In a large bowl, whisk together the flour, pumpkin spice, baking soda, baking powder and salt; set aside.
In a medium bowl, whisk together the pumpkin, sugar, brown sugar, oil, eggs and vanilla extract until well combined.
Pour the pumpkin mixture into the flour mixture and stir until just combined.
Divide the batter evenly into the prepared muffin cups, each will be quite full.
Sprinkle the pumpkin seed mixture evenly over the tops of the muffins.
Cut the end of the piping bag, then insert into the center of the muffins and pipe a dollop of cream cheese filling into each muffin.
Bake in the preheated oven for 5 minutes, then turn the oven down to 350°F (180°C), or 160°C for a fan oven and continue baking an addition 15 minutes, or until the muffins are domed and a toothpick inserted into the center comes out clean.
Allow to cool for 5 minutes in the pan before transferring to a wire rack to cool completely.