Set the oven racks to the upper-middle and lower-middle positions. Preheat to 350ºF (177ºC).
Line two large baking sheets with parchment paper.
In a medium bowl whisk together flour, cinnamon, ginger, nutmeg, cloves, allspice, baking soda, and salt.
In a stand mixer fitted with a whisk attachment (or hand mixer) add eggs and sugar to the mixing bowl. Whisk on medium-high speed until pale and fluffy, 3 minutes.
Add the pumpkin puree, melted butter, and vanilla, whisk on medium speed until combined, 30 seconds.
On low speed, slowly add the flour mixture until combined with the wet ingredients, about 30 seconds.
Add the batter to a piping bag fitted with a large round tip (806 size recommended). Pipe about 1-tablespoon sized amounts of batter (about 1 ½ inch circles) onto the parchment paper spaced at least 1-inch apart. About 20 cookies should fit on a large baking sheet. Repeat with the remaining batter on the other pan.
Transfer the baking sheets to the oven and bake until the cakes are set, 10 to 12 minutes. Rotate halfway through and switch the locations.
Cool the cakes on the baking sheet for 5 minutes and then remove and transfer to a cooling rack.
Cream Cheese Filling
In a stand mixer fitted with the whisk attachment (or hand mixer), beat 4 tablespoons softened butter and powdered sugar on medium-high speed until pale and fluffy, 2 minutes.
Add cream cheese, one piece at a time and mix until smooth.
Add the cinnamon and mix until incorporated.
Spread about 1 to 2 teaspoons of frosting on the bottom half of a cake, and then sandwich together with another half. Lightly press until the filling just reaches the edges.
Enjoy within the next same day, or refrigerate any leftover whoopie pies. Bring pies to room temperature before serving.
Larger cookies can be made by piping 2 tablespoon-sized mounds and using a spoon to spread into a circle. Bake for about 12 minutes.
Homemade pumpkin spice can be used. Add 1 ¾ to 2 teaspoons of the blend to the mixture instead of the individual spices in the ingredient list.
Make-ahead: Cakes and frosting can be made a day ahead and stored separately in an airtight container. Allow the frosting to warm slightly at room temperature before filling.
Storage: Unfrosted whoopie pies can be stored in a container on the countertop for up to 3 days. Frosted cookies should be stored in a container in the refrigerator for up to 5 days. Allow pies to come to room temperature before serving.
Recipe adapted from The Perfect Cookie, America’s Test Kitchen