In a large mixing bowl, combine all-purpose flour, baking soda, ground ginger, ground cinnamon, ground nutmeg, and brown sugar. Add unsalted butter and mix until the texture resembles coarse crumbs.

Incorporate the egg and molasses, stirring until the dough is well-combined and thick yet pliable. This gingerbread whoopie pies dough should feel slightly sticky but manageable.

Preheat your oven to 350°F (175°C). Using a cookie scoop or tablespoon, drop heaping balls of dough onto a baking sheet lined with parchment paper, spacing them about 2 inches apart.

Bake the cookies for 10 minutes, until the edges are set and the tops appear slightly puffed.

Once baked, remove the gingerbread whoopie pies from the oven and let them cool on the baking sheet for 5 minutes. Transfer the cookies to a wire rack to cool completely.

In a medium bowl, beat together cream cheese, powdered sugar, ground cinnamon, and ground nutmeg using an electric mixer. Mix until smooth and fluffy—this should take about 3-4 minutes.

Once your gingerbread cookies are completely cooled, spread a generous dollop of the spiced cream cheese filling on the flat side of one cookie and gently press another cookie onto the filling.

For the best flavor and texture, place the assembled gingerbread whoopie pies in the refrigerator for about 1 hour.