Prepare the Baking Sheets: Preheat the oven to 350°F. Line two baking sheets with parchment paper and set them aside.
Mix the Dry Ingredients: In a medium bowl, whisk together the flour, baking powder, baking soda, cinnamon, ginger, nutmeg, cloves, and salt until evenly combined.
Prepare the Pumpkin Mixture: In a large bowl, whisk together the brown sugar and vegetable oil. Add the pumpkin purée, eggs, and vanilla extract. Whisk until smooth and well combined.
Combine the Wet and Dry Ingredients: Gradually add the dry ingredients to the pumpkin mixture. Stir gently until the flour is just incorporated. Do not overmix the batter.
Portion the Pumpkin Batter: Use a cookie scoop to place evenly sized portions of batter onto the prepared baking sheets, leaving space between each one.
Bake the Pumpkin Cakes: Bake for 12–14 minutes, or until the tops are set and the cakes spring back lightly when touched. Allow them to cool on the baking sheet briefly before transferring them to a wire rack.
Make the Cream Cheese Filling: Beat the softened cream cheese and butter until smooth and fluffy. Gradually add the powdered sugar, vanilla extract, and salt. Continue mixing until creamy and smooth.
Fill the Whoopie Pies: Once the pumpkin cakes are completely cool, turn half of them flat-side up. Pipe or spread cream cheese filling onto each cake.
Assemble and Chill: Place another pumpkin cake on top of each filled cake and gently press together. Refrigerate the assembled whoopie pies for about 30 minutes before serving.