Preheat oven to 350 F. Blend oats in a blender to create oat flour, then combine in a bowl with baking powder, pumpkin pie spice, baking soda and salt.
Meanwhile, combine Greek yogurt, pumpkin puree, eggs, maple syrup and vanilla in another large bowl. Add dry ingredients to wet ingredients and fold in just to combine.
Next make the cream cheese filling. Blend cream cheese, icing sugar, flour and milk until smooth with beaters, then add mixture to a piping bag or ziploc bag with the corner cut off.
Divide muffin batter among 12 greased cups in your muffin tin, then add a dollop of cheese cheese filling to each and sprinkle pumpkin seeds overtop.
Bake for 20-25 minutes or until a toothpick inserted in the middle of a muffin comes out clean (I usually check at the 20 minute mark).
Let cool a few minutes in the muffin tin before transferring to a wire rack to cool completely. Store muffins on the counter up to 5 days or in the fridge up to 10 days.