Preheat oven to 350 Fahrenheit (or 180 Celsius)
Make Cream Cheese Filling: In the medium bowl, beat cream cheese until smooth. Add in sugar, egg yolk, and beat until well combined. Then put the cream cheese mixture in the piping bag.
Dry ingredients: In a large bowl, combine flour, baking soda, baking powder, salt, ground cinnamon, ground cloves, and ground ginger.
Wet ingredients: In a medium bowl, combine the fresh pumpkin puree, melted butter, sugar, egg, and vanilla extract. Whisk together and then add the boiled pumpkin puree. Mix well.
Pour the wet ingredients into the dry and stir until everything is just combined and you have a nice thick batter. Then fill muffin tins 3/4 full.
Add cream cheese mixture in the middle and top of each muffin. Top with pumpkin seeds (if desired!).
Bake for 18 to 20 minutes or until set through and a toothpick comes out clean. Let cool on a wire rack.
Serve and enjoy!