Start by preheating your oven to 350°F and lining two 12-cup muffin tins with paper liners.
In a large bowl, whisk together the flour, sugar, cocoa powder, baking soda, baking powder, and salt. Make sure to break up any cocoa powder lumps – they can be sneaky and leave bitter spots in your cupcakes.
Brew your coffee and keep it hot – this is important because hot coffee helps bloom the cocoa powder, making the chocolate flavor deeper and richer.
In a separate bowl, whisk together the eggs, milk, oil, and vanilla until well combined. The mixture should be smooth and uniform in color.
Pour the wet ingredients into the dry ingredients. Start mixing with a whisk or spatula until mostly combined – you’ll still see some flour streaks and that’s okay.
Add the hot coffee and mix until the batter is smooth. It will be quite thin, almost like chocolate soup – don’t worry, that’s exactly what you want!
Fill each cupcake liner about 2/3 full (about 3 tablespoons of batter). I use an ice cream scoop to make this easier and keep them uniform.
Bake for 18-20 minutes. You’ll know they’re done when a toothpick inserted in the center comes out clean and the tops spring back when lightly pressed. The surface should look set and no longer shiny.
Let them cool in the pans for about 5 minutes (they’re fragile when hot), then transfer to a wire rack to cool completely before frosting.