Preheat oven to 425F. Place nine muffin liners in a 12-cup muffin pan.
In a medium-sized bowl, whisk together the almond flour, cornstarch, pumpkin spice, cinnamon, baking powder and salt.
In a large bowl, use an electric mixer on high speed to beat together the eggs and sugar until pale and just starting to thicken. (About 1 minute).
Add the pumpkin, maple syrup, oil and vanilla and mix until combined.
Add the dry ingredients to the wet mixture and use a spatula to fold in until just combined.
In a separate medium-sized bowl, add the cream cheese, powdered sugar, milk and vanilla. Use an electric mixer to beat together until smooth and creamy. Transfer the cream cheese filling to a piping bag.
Divide the batter into the 9 muffin liners, filling them almost to the top. Use the back of a spoon to smooth out the tops of the batter.
Pipe some of the cream cheese filling into the center of the batter for each muffin and finish with a dollop on top.
Sprinkle some pumpkin seeds on top of each muffin, around the dollop of cream cheese.
Bake at 425F for 5 minutes, then reduce the temperature to 350F and bake for another 16-18 minutes, or until a toothpick inserted into a muffin comes out with just a few crumbs on it.
Let cool in the pan for 10 minutes, then transfer to a wire rack to cool completely.
Notes
Beat sugar and eggs. Mixing together the sugar and eggs until pale and just starting to thicken is key to the rise and texture of these muffins. I prefer to use an electric mixer, but you can also use a whisk, it'll just take longer.
Cream cheese filling. Don't just dollop some cream cheese on top of the muffin batter. Make sure you insert the piping tip into the batter and dispense some of the cream cheese into the center, before finishing with a dollop on top.
Piping bag. I used a piping bag with a large, round piping tip to add the cream cheese filling to the center of the muffins. You can also just use a ziploc bag with one of the corners snipped off.
Makes 9 muffins. In order to keep these muffins tall, I divided the batter into 9 muffin cavitites instead of 12.