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Preheat the oven to 350 degrees. Line 20 to 22 muffin cups with paper liners and set aside.
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Whisk the coffee (or wateand cocoa powder in a small mixing bowl. Cool to room temperature.
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Sift the flour, baking soda, baking powder, and salt together into a second mixing bowl and set aside.
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Beat the butter, sugar, eggs, and vanilla together in a large mixing bowl with an electric mixer set to high speed. Continue beating on high until mixture is light and fluffy, scraping down the sides and bottom of the bowl as needed—this will take about 5 minutes.
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Turn mixer to low and add the flour mixture in 3 additions, alternating with the cocoa mixture, beginning and ending with the flour.
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Divide batter among the prepared muffin cups, filling each 2/3 full. Bake 15 to 20 minutes, until a cake tester inserted into the center of the cupcakes comes out clean.
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Cool cupcakes completely in pan for 20 minutes then remove to a wire rack to cool completely before filling and frosting.