Preheat the oven to 350°F. Line 12 cupcake cups with liners. Bring the Guinness and butter to a simmer in a medium saucepan over medium heat. Add the cocoa powder and chocolate chips and whisk until the mixture is smooth. Set aside to let cool slightly.
Whisk the flour, sugar, baking soda and salt in a large bowl. Set aside.
Using an electric mixer, beat the eggs, greek yogurt and vanilla extract on medium speed until combined. Add the chocolate/Guinness mixture to this and beat until just combined. Reduce the speed to low and gradually add the flour mixture until just combined. Use a rubber spatula and fold the batter until completely combined.
Scoop the batter into the cupcake liners until each one is about ⅔ of the way full. The batter will be slightly thicker than a typical cake batter.
Bake 17-19 minutes, or until a toothpick inserted into the center of the cupcake comes out clean. Cool the cupcakes on a wire rack.
Place the chocolate chips in a medium heatproof bowl. Heat the heavy cream until simmering and pour it over the chocolate. Let sit for 2-3 minutes and then stir it.
Add the butter, whisky and vanilla extract and stir until combined. Let the ganache cool till thickened, but still soft enough to pipe out.
Using a knife, cut the centers out of the cooled cupcakes. (I take a knife and cut about a 1 in diameter circle, angling the knife in slightly so it comes out evenly). Put the ganache in a piping bag or a sandwich bag the corner cut out. Fill in the holes of the cupcakes.
Using the whisk attachment of a mixer, whip the butter on medium-high speed for 5 minutes, scraping the sides of the bowl after every minute. Reduce the speed to medium-low and gradually add the powdered sugar until it is all incorporated. Add the Baileys, increase the speed to medium-high and whip for another 2-3 minutes until it is light and fluffy.
Using a piping bag with a large decorating tip, or an offset spatula, frost the cupcakes. Decorate how desired.
The Guinness helps just intensify the chocolate flavor. But if you don't want to use it, just use freshly brewed coffee.
If you don’t have Greek yogurt, you can either replace with sour cream.
All refrigerated items should be at room temperature, which helps the batter mix easily and evenly.
Use natural cocoa powder vs Dutch-processed cocoa powder as natural cocoa powder isn’t as intense of a flavor.
You may not realize this but baking powder and baking soda actually expires pretty quickly. Use baking soda that is less than six months old since it has been opened. If you use older baking powder, it won’t be powerful enough to help leaven the donuts. You can test it by stirring half a teaspoon of baking powder into a cup of hot water. It will immediately start to fizz and release carbon dioxide gas if it’s still fresh enough to use.
When adding the batter to the muffin tin, don’t fill more than ⅔ of the way as they do rise.
You know the cupcakes are done when you insert a toothpick in the center and it comes out clean.
Don't let the ganache cool too much, otherwise you won't be able to pipe it out.
Allow the cupcakes to completely cool before adding the ganache and frosting, otherwise it will melt.