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Preheat oven to 350 degrees F. Line two muffin pans with cupcake liners.
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In a medium bowl sift together flour, baking powder, baking soda and salt. In a measuring cup, dissolve the instant coffee in the hot coffee and let cool slightly. Add the milk to the coffee.
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In the bowl of an electric mixer, cream butter and sugars until pale and fluffy, about 5 minutes on medium speed. Add eggs one at a time, beating until combined after each addition. Beat in vanilla extract.
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Reduce mixer speed to low and slowly add about half of the flour mixture. Add half of the milk, then the rest of the flour and the rest of the milk. Beat until just combined. Scrap down the side of the bowl as needed.
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Pour batter into prepared pans. Fill liners about 2/3 full. Bake cupcakes until lightly golden or a toothpick inserted into the center comes out clean, about 12-14 minutes.
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Cool in pan 1-2 minutes, then remove cupcakes from pan and finish cooling on a wire rack.