Preheat oven to 350°F (175°C). Line baking sheets with parchment paper.
In a large bowl, whisk together the flour, baking soda, salt, ginger, cinnamon, cloves, and nutmeg.
In a separate bowl, cream together the softened butter and brown sugar until light and fluffy.
Beat in the molasses and eggs one at a time, then stir in the milk.
Gradually add the dry ingredients to the wet ingredients, mixing until just combined.
Drop rounded tablespoons of dough onto the prepared baking sheets, about 2 inches apart.
Bake for 10-12 minutes, or until the edges are set and the centers are slightly soft. Do not overbake.
Let the whoopie pies cool on the baking sheets for a few minutes before transferring them to a wire rack to cool completely.
Make the Cream Cheese Frosting
In a large bowl, beat the softened cream cheese and butter until smooth and creamy.
Gradually add the powdered sugar, beating until well combined and smooth. Stir in the vanilla, ginger, and cinnamon.
Assemble the Whoopie Pies
Spread a generous amount of frosting onto the flat side of one whoopie pie. Top with another whoopie pie, pressing gently to sandwich the frosting.
Repeat with the remaining whoopie pies.
Store whoopie pies in an airtight container in the refrigerator.
Notes
These gingerbread whoopie pies are best enjoyed within 2-3 days. For a more intense gingerbread flavor, you can let the dough chill for 30 minutes before baking.