Preheat the oven to 350 degrees F and line a 12-cup muffin pan with paper liners. Set aside.
For the cupcakes: Whisk together the flour, baking soda and salt in a medium bowl and set aside. Heat the milk in a small saucepan until hot, but not boiling, and pour the milk over the cocoa powder in a large bowl. Whisk the mixture until it is smooth and cools slightly. Add the sugar, oil, vanilla and egg to the milk mixture and whisk until smooth. Add the flour mixture, and stir, with a rubber spatula, until well combined (take care not to overmix).
Divide the batter evenly among the prepared muffin cups. Bake until the tops spring back when pressed lightly, 20 to 22 minutes. Transfer the pan to a rack and let cool for 5 minutes, then transfer the cupcakes to the rack to cool a bit more, about 20 minutes.
Meanwhile, make the wine syrup: Bring the wine and sugar to a boil over medium heat in a small saucepan. Reduce the wine to 1/2 cup, 12 to 15 minutes. Transfer the wine syrup to a small bowl.
While the cupcakes are still slightly warm, poke the top of each 2 times with a fork and slowly drizzle in a generous teaspoon of the wine syrup. Set aside the remaining wine syrup.
For the ganache: Pour the cream into the saucepan used for the wine syrup and bring it to a simmer. Put the chocolate in a medium bowl. Pour the cream over it and whisk until smooth. Add the remaining wine syrup and stir until combined. Let the ganache cool until thickened slightly and the consistency of heavy cream, about 3 minutes.
Spoon a tablespoon of ganache on each cupcake and use the back of the spoon to spread it evenly. Place the cupcakes on a rack and allow the ganache to set, about 15 minutes.
When measuring flour, we spoon it into a dry measuring cup and level off excess. (Scooping directly from the bag compacts the flour, resulting in dry baked goods.)
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