Preheat your oven to 350°F (175°C).
In a bowl, whisk together the flour, ginger, cinnamon, nutmeg, baking soda, and salt.
In a larger mixing bowl, cream together the softened butter and brown sugar until light and fluffy.
Add the egg and vanilla extract to the butter mixture and mix until combined.
Gradually mix in the dry ingredients into the wet mixture until just combined.
In a separate bowl, blend the softened cream cheese, powdered sugar, and vanilla extract for the filling until smooth.
Scoop out small amounts of dough and flatten each piece in your palm, placing a teaspoon of cheesecake filling in the center before folding the dough around it.
Place the filled cookies on a baking sheet lined with parchment paper, spacing them about two inches apart.
Bake in the preheated oven for 12-15 minutes, or until the edges are slightly golden.
Allow the cookies to cool on the pan for a few minutes before transferring them to a wire rack to cool completely.