Preheat oven to 350°F (175°C). Line baking sheets with parchment paper.
In a large bowl, whisk together the flour, baking soda, cinnamon, nutmeg, cloves, and salt.
In a separate large bowl, cream together the softened butter, brown sugar, and granulated sugar until light and fluffy.
Beat in the eggs one at a time, then stir in the milk, pumpkin puree, and vanilla extract.
Gradually add the dry ingredients to the wet ingredients, mixing until just combined. Do not overmix.
Drop rounded tablespoons of batter onto the prepared baking sheets, about 2 inches apart.
Bake for 10-12 minutes, or until the edges are lightly golden and a toothpick inserted into the center comes out clean. Let cool on the baking sheets for a few minutes before transferring to a wire rack to cool completely.
While the cookies cool, prepare the frosting. In a large bowl, beat together the softened cream cheese and softened butter until smooth and creamy.
Gradually beat in the powdered sugar until well combined. Stir in the vanilla extract and milk, adding more milk if needed to reach desired consistency.
Once the cookies are completely cooled, spread frosting on the flat side of one cookie and top with another cookie to create a sandwich.
Repeat with remaining cookies. Store whoopie pies in an airtight container in the refrigerator.
Notes
These pumpkin whoopie pies are best enjoyed within 3-4 days when stored in the refrigerator.