Preheat oven to 350°F. Line 2 large baking sheets with parchment paper. Set aside.
In a medium bowl use a whisk to sift flour, pumpkin pie spice, baking powder, baking soda and salt.
In a separate large mixing bowl use an electric mixer to cream together butter, granulated sugar and brown sugar with vanilla extract. Beat on medium-high speed for 2-3 minutes or until fluffy.
Add the eggs one at a time, beating well after each addition. Add canned pumpkin puree, mix to fully combine.
Lower the speed of the mixer and gradually add the sifted flour mixture to the pumpkin mixture. Stop and scrape the sides of the bowl as needed. Beat until fully moistened.
Using a 2 Tbsp scoop or a small ice cream scoop to divide the dough onto the sheet pans. Leave at least 2-inches between to allow for spreading.
Bake for 10 minutes. Cool on pan for 5 minutes then remove to a wire rack to cool completely.
Cream Cheese Filling: Using an electric mixer, beat together cream cheese, butter and vanilla on medium-high speed until combined. Lower the speed of the mixer and gradually add powdered sugar. Beat in marshmallow fluff at the end, just until smooth.
Divide cream cheese filling between half of the cooled cookies. Slather one flat side then place another on top of the filling to sandwich whoopie pies together. (You can use an icing spatula or a piping bag to pipe the filling.)
Store whoopie pies in an airtight container chilled in the fridge for up to 1 week. Place wax paper between if stacking.
Notes
Pumpkin Pie Spice - What's in pumpkin pie spice? It's a blend of ground cinnamon, ground nutmeg, ground ginger, allspice and cloves. It adds a depth of flavor that makes it my number one choice for these beauties. You could substitute ground cinnamon in a pinch.
Cream Cheese Frosting - You can sandwich these together using a classic cream cheese frosting. See my recipe for homemade cream cheese frosting here.
Nuts - You could add 1/2 cup of chopped pecans or walnuts to the filing for a crunchy texture.
Use a Scoop for Uniformity - I highly recommend using an ice cream scoop to keep the whoopie pies uniform in shape. The most common ice cream scoop we all use is for, well, ice cream. It's a 4 ounce size. The size I recommend for these is a 2 ounce or one that's half that size. You can also use a 1/4 cup measuring cup or 2 1/2 tablespoons or a cookie scoop.
Yield May Vary - The amount of pumpkin whoopie pies yielded depends on how the batter is divided. You can make these larger or smaller, depending on how many servings you need. When changing the size, it may also affect the baking time. Do a trial run and bake one, then proceed based on those results.