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Preheat oven to 350 degrees. Line 18 muffin cups with cupcake liners and set pan aside.
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Sift the flour, cocoa powder, baking powder, and salt together in a medium mixing bowl. Set aside.
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In the bowl of a stand mixer fitted with the paddle attachment cream the butter and sugars together until light and fluffy, about 2 minutes on medium speed. Scrape down the sides and bottom of the bowl; turn mixer to low and beat in eggs and egg yolk, one at a time, beating well after each addition. Beat in vanilla extract.
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Combine the coffee and whole milk in a glass measuring cup. With mixer on low, add the dry ingredients in three additions, alternating with the milk-coffee mixture, beginning and ending with the dry ingredients. Mix until just combined.
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Divide batter evenly between prepared muffin cups, filling each about 2/3 of the way through. Bake for 18 to 20 minutes, until the cupcakes spring back when pressed gently with your fingertip. Allow to cool in muffin tins for 10 minutes, then remove to a wire rack to cool completely before filling and frosting.