Add 1/2 a cup of warm melted butter, 1 tsp of vanilla and the molasses to a large bowl and mix well to combine. The heat from the warm butter will make it easier to mix into the molasses.
Add the sugar and egg to the bowl and mix to combine.
Add the pumpkin puree and mix to combine.
Place a large sieve over the bowl and add the flour, pumpkin spice, salt, baking powder and baking soda. Use a spoon to stir the dry ingredients through the sieve into the wet ingredients below.
Mix the wet and dry ingredients together just until combined. Do not overmix.
Line a baking sheet with parchment paper and a tablespoon of the cookie dough into a ball and place it on the baking sheet. Repeat until the cookie sheet has 12 cookies. This pumpkin cream cheese cookie recipe will make about 2 1/2 dozen so set the rest of the cookie batter aside until these are done baking.
Bake for 7 minutes and then remove from oven. Using the end of a wooden spoon or your thumb (be careful aka quick the cookies are hot) push a thumb-sized hole in the centre about 1/2 way down to make a space for the cream cheese filling.
Return the cookies to the oven and continue to bake for another 7 or 8 minutes or until the cookies are firm to touch but have not started to brown.Remove the cookies from the oven and let them cool completely on a cooling rack. If the centre of the cookie has puffed back up use the end of the spoon again or your thumb to once again make a divot in the centre of the cookie. Do this before the cookies cool.
For the Filling
Add the cream cheese, 1/4 cup of room temperature butter, and 1 tsp of vanilla to a large bowl to make the filling. Beat on high using a hand or stand mixer until the mixture is smooth and well blended.
Gradually add the powdered sugar into the bowl using the mixer and continue mixing until all the powdered sugar is combined and the filling is smooth and creamy.
Assembly
Once the cookies are completely cool use a piping bag or a small spoon to fill the centre with the cream cheese filling. Let the cookies set on the counter or place them in the fridge to set the cream cheese. These cookies don't stack all that well when the cream cheese is soft so I recommend storing them in the fridge. Once the cream cheese is set the cookies can be carefully stacked.
Notes
Storage and FreezingThese Pumpkin Cheesecake Cookies can be stored for up to 1 week in the fridge or for 3 months in the freeze. Thaw frozen cookies before serving either by letting them sit on the counter for about 1/2 and hour before serving or overnight in the fridge.