Preheat the oven to 350°F. Place 24 cupcake liners into 2 standard muffin pans. Set aside.
In a medium bowl, combine the all-purpose flour, baking soda, baking powder, salt, cinnamon, ground ginger, nutmeg, and ground cloves. Set your dry ingredients aside.
In the bowl of a stand mixer fitted with a paddle attachment, beat the unsalted butter, granulated sugar, and brown sugar on low speed for 1 to 2 minutes or until light and fluffy.
Beat in your egg until fully incorporated. You may need to scrape down the sides of your mixing bowl, and the paddle attachment, before proceeding to ensure that all the ingredients are incorporated.
While your mixer is on low, slowly add your unsulphured molasses and vanilla extract to the mixer and continue to mix until all your ingredients are fully incorporated. You will need to scrape down the sides of your bowl and paddle attachment again before moving on.
Next, add the dry ingredients to the batter, a little at a time, allowing the flour to incorporate before adding more while you continue to stir on low. You will want to stop your mixer once all the flour has been incorporated. You do not want to overmix your batter. You will need to scrape down your bowl again at this point.
Lastly, while your mixer is on low speed, you will slowly pour the boiling water into the batter until all the water has been added. You will need to increase your speed to medium-low for 30 to 45 seconds just to make sure that you have a fully incorporated and smooth batter.
You will need to remove your paddle attachment from the bowl to scrape down the sides and fold your batter a few times to ensure that all of the batter is evenly combined.
Using a 2-inch cookie scoop, fill each of the prepared muffin pans no more than ⅔ full. This batter will rise a lot in the oven, so you do not want your cupcakes to overflow in the pan.
Bake for 22 to 24 minutes or until a toothpick inserted into the center comes out clean.
Allow these gingerbread cupcakes to cool in the pan for 10 minutes, then transfer them to a wire rack to cool completely on the counter.