Preheat your oven to 350°F (175°C) and line two baking sheets with parchment paper.
In a medium bowl, whisk together the flour, baking soda, ground ginger, ground cinnamon, ground nutmeg, and salt; set aside.
In a large mixing bowl, cream together the softened butter and brown sugar until light and fluffy.
Beat in the egg, then add the molasses and vanilla extract, mixing until well combined.
Gradually add the dry ingredient mixture to the wet ingredients, mixing until just combined.
Drop tablespoon-sized mounds of batter onto the prepared baking sheets, leaving space between each mound as they will spread while baking.
Bake for 10-12 minutes, or until the edges are firm and the centers are slightly soft. Remove from the oven and let cool on the baking sheets for 5 minutes before transferring to a wire rack to cool completely.
While the whoopie pies cool, prepare the cream cheese filling. In a medium bowl, beat together the softened cream cheese and butter until smooth and creamy.
Gradually add the powdered sugar and vanilla extract, continuing to beat until well blended and fluffy.
Once the whoopie pies are completely cool, pair them into matching sizes, and spread a generous amount of cream cheese filling on the flat side of one cookie before gently pressing the matching cookie on top.
Repeat with the remaining cookies until all are filled.
Notes
Dust the assembled whoopie pies with a light sprinkle of powdered sugar and serve them on a festive platter.