Preheat the oven to 350ºF and line a muffin tin with 12 cupcake liners.
Beat together the melted butter, molasses, and brown sugar.
Add in the egg and beat until mixed.
In a large bowl, the all-purpose flour, baking powder, baking soda, salt, ginger, cinnamon, nutmeg, and cloves are then mixed together and set aside.
The semi-sweet chocolate squares are melted following the melting directions according to your chocolate of choice.
Set the melted chocolate aside and allow it to cool.
Slowly beat the flour mixture into the wet ingredients a little at a time.
After adding about half of the flour mixture, add the cooled melted chocolate to the batter.
Add the remaining flour to the batter followed by the milk.
The batter will be very thick for these chocolate gingerbread cupcakes and that is okay! They will have a wonderful gingerbread texture after baking.
Divide the cupcake batter equally between 12 liners before baking. As stated above, the batter will be very thick, and using a cookie scoop will make it easy to equally divide the batter.
Once these cupcakes are baked in the preheated oven for about 18-20 minutes they are removed and allow them to cool completely before frosting.
Gingerbread Frosting
Beat together the softened butter and the molasses until creamy.
Beat in the ginger and the confectioners sugar.
The frosting will be thick, add the milk 2 tablespoons at a time until the frosting is smooth and soft enough to pipe.
Frost the cupcakes using a piping tip and bag.
Chocolate Ganache
Heat the heavy cream in a saucepan just until a low boil.
Remove from the heat and add the chocolate chips or squares.
Allow it sit for a few minutes to allow the chocolate to melt.
Stir the chocolate until smooth.
Drizzle the chocolate ganache over the frosting.
Store in an airtight container.
Notes
Using a cookie scoop to fill the cupcake liners with batter will make it easy to scoop and distribute the batter evenly.