Preheat the oven to 325°F (163°C). Line a 9x9-inch pan with parchment paper, leaving overhang for easy lifting.
Make the base: In a bowl, whisk flour, spices, baking soda, and salt.
In another bowl, whisk melted butter, brown sugar, molasses, egg, and vanilla until smooth. Stir the dry ingredients into the wet until just combined.
Press the gingerbread mixture evenly into the prepared pan. Use damp fingers or the back of a spoon to smooth the top.
Par-bake the base for 8–10 minutes.
It should look slightly set but not fully baked.
Make the cheesecake layer: Beat cream cheese and sugar on medium speed until smooth and fluffy, about 2 minutes. Add eggs one at a time, mixing just until combined. Mix in sour cream, vanilla, and a pinch of salt.
Pour the cheesecake batter over the warm base.
Tap the pan gently to release air bubbles.
Bake for 28–34 minutes, until the edges are set and the center has a slight jiggle. Avoid overbaking.
Cool on a wire rack for 1 hour, then refrigerate at least 3 hours (overnight is best) to set.
Lift out using the parchment, slice into bars with a hot, clean knife, and garnish as desired.