Preheat your oven to 350°F (175°C) and prepare a baking sheet with parchment paper.
In a medium bowl, whisk together the flour, baking soda, ground ginger, cinnamon, nutmeg, and salt.
In a large bowl, cream together the softened butter and brown sugar until light and fluffy.
Add the egg and vanilla extract to the butter-sugar mixture, mixing until fully combined.
Gradually mix in the dry ingredients until just combined.
In a separate bowl, combine the softened cream cheese, powdered sugar, and ground ginger for the filling until smooth.
Scoop out small portions of cookie dough, and flatten each ball slightly before adding a dollop of the cream cheese mixture in the center.
Seal the filling within the dough by carefully folding the edges over and rolling into a ball again.
Place the prepared cookies on the lined baking sheet, leaving enough room for spreading between each.
Bake for about 12-15 minutes or until the edges are lightly golden.
Let the cookies cool on the baking sheet for 5 minutes before transferring to a wire rack to cool completely.