Preheat oven to 350°F. Line 2 large baking pans with parchment or a silicone baking mat. Set aside.
In a medium-size mixing bowl, use a whisk to sift together flour, pumpkin pie spice, baking powder, baking soda and salt.
In a separate mixing bowl use an electric mixer to cream together butter, granulated and brown sugars with vanilla. Beat on medium-high for 2-3 minutes until fluffy.
Add the eggs one at a time, beating well after each addition. Add pumpkin puree, mix well.
Lower the speed of the mixer and gradually add the dry ingredients. Stop and scrape the sides of the bowl as needed. Beat until fully moistened.
Using a 2 Tbsp or a small 2 oz ice cream scoop, divide the dough, leaving at least 2 inches between to allow for spreading. Bake for 10 minutes. Cool on pan for 5 minutes then remove to a cooling rack to cool completely.
To make the filling, using an electric mixer, beat together cream cheese, butter and vanilla until combined. Lower the speed of the mixer and gradually add powdered sugar. Beat in marshmallow fluff at the end, until smooth.
Divide filling between whoopie pies and sandwich together.
Store in an airtight container chilled for up to 1 week. Place wax paper between if stacking.