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To prepare cupcakes: Preheat oven to 350°F. Line 2 standard-size muffin pans with 24 cupcake liners.
In a medium bowl, mix flour, cocoa, baking powder, baking soda and salt. In a large bowl, beat 3/4 cup butter and granulated sugar with an electric mixer on medium-high speed until smooth. Beat in sour cream. Beat in eggs, one at a time. With the mixer on low speed, beat in flour mixture and food coloring, alternating with milk. Spoon into cupcake liners, filling each about 2/3 full.
Bake until a toothpick inserted in the centers of the cupcakes comes out clean, about 23 minutes. Remove from the pan; cool completely on a wire rack.
To prepare frosting: Beat cream cheese and butter until smooth. With the mixer on low speed, beat in confectioners' sugar, then vanilla. Spread or pipe onto cooled cupcakes.