Preheat the oven to 350 degrees F. Line a 12-cup muffin pan with paper liners. In a medium bowl combine the flour, baking soda, ginger, cinnamon, nutmeg, cloves and salt.
Using an electric mixer, beat together the butter and dark brown sugar until light and fluffy.
Beat in the vanilla, molasses and egg until combined. Add the milk, alternating with the flour mixture until everything is combined.
Divide the batter evenly among the prepared muffin pan, fill the muffin cups 2/3rds of the way full.
Transfer to the oven and bake until a toothpick inserted into the center of each comes out with moist crumbs attached, 18-22 minutes. Let cool before frosting.
Add 1 stick butter to a skillet set over medium heat. Brown butter lightly until it smells toasted, about 2-3 minutes.
Stir often. Remove from the heat and transfer the butter to the mixing bowl, let cool until it’s room temp. Add the remaining stick of butter and beat until is light and fluffy.
Mix in the honey, vanilla, and cinnamon and beat until evenly incorporated. Very gradually add the powdered sugar until it’s fully blended and smooth.
Apply the Brown Butter Cinnamon Frosting to the cooled Gingerbread Cupcakes with a butter knife, small spatula, or a piping bag and tip. Decorate cupcakes as desired. Enjoy!