Preheat oven to 375 degrees F and line a 12-count muffin and 6-count muffin tin with paper liners.
In a medium-sized bowl, whisk together flour, pumpkin spice, cinnamon, baking powder, baking soda, and salt. Set aside.
With a stand mixer, mix together the coconut oil and sugars until creamy, about 1-2 minutes. Add egg one at a time until well combined and then the pumpkin purée, maple sugar, vanilla extract and milk. Scrape down sides if needed.
Slowly add dry ingredients to the wet pumpkin mixture just until combined. Do not over mix.
Scoop about 2 tablespoons of batter into each prepared muffin liner.
For the cream cheese filling: With a hand mixer, mix the cream cheese with the sugar and vanilla extract until creamy.
Spoon or use a pastry bag to fill each crater with a heavy amount of the cream cheese mixture. Cover with more of the pumpkin batter about ¾ of the way. You want some of the cheesecake to be poking through at the top.
Bake in the oven at 375 degrees for 20-25 minutes or until golden brown and a toothpick inserted in the center comes out clean.