Preheat oven to 350°F. Line a 12-cup muffin pan with cupcake liners.
In a medium bowl, whisk together flour, baking powder, baking soda, salt, ginger, cinnamon, cloves, and nutmeg.
In a stand mixer fitted with the paddle attachment, cream butter and brown sugar for 2–3 minutes until light and fluffy.
Add eggs one at a time, mixing well after each addition.
Add molasses and vanilla extract. Mix until combined.
Add half the dry ingredients and mix on low speed.
Add sour cream and milk, followed by the remaining dry ingredients. Mix just until combined.
Divide batter evenly between cupcake liners, filling each approximately two-thirds full.
Bake for 18–22 minutes, or until a toothpick inserted into the center comes out clean or with a few moist crumbs.
Cool in the pan for 5 minutes, then transfer to a wire rack to cool completely before frosting.