There are plenty of chocolate cupcake recipes out there to choose from, but this indulgent recipe might just be my favorite. These Double Chocolate Cheesecake Cupcakes have a deep, dark chocolate flavor and are topped with a decadent dark chocolate ganache, delivering a double hit of chocolate in every bite. They are also filled with a vanilla bean cream cheese filling, adding just the right amount of contrast to all that chocolate.

The cupcake recipe is a classic dark chocolate cupcake, made with plenty of unsweetened cocoa powder to give it a deep and bittersweet flavor. If you’re a regular baker of chocolate cupcakes, you’ll also notice that there are equal amounts of cocoa powder and flour in this recipe. This creates a light and tender cake, rather than a dense and brownie-like one. This lighter texture is important because it lets the cake stand up to the rich filling and topping without the whole dessert seeming to heavy.

The cheesecake filling is easy to make, with just butter, cream cheese, confectioners’ sugar and vanilla. Vanilla bean paste is going to give your cheesecake filling a beautiful finished look, however extract can be substituted and will still provide a nice vanilla flavor. The filling isn’t overly sweet, so you should be able to taste the tang of cream cheese in every bite.

Chocolate ganache is the topping for these cupcakes. It is easy to make and produces a topping that is velvety smooth and rich. You can use chopped chocolate if you have a large block at home, but dark or semisweet chocolate chips will work just as well. Once the ganache is made, you’ll need to allow it to cool before you can pipe it onto your cupcakes. Give it a stir occasionally to check the consistency, but it should take somewhere from 30 – 45 minutes to thicken up enough to pipe.

Double Chocolate Cheesecake Cupcakes
Cupcakes
3/4 cup all purpose flour
3/4 cup cocoa powder, unsweetened
1/2 tsp baking powder
1/4 tsp salt
3/4 cup butter, room temperature
1 cup sugar
3 large eggs
1 tsp vanilla extract
1/2 cup sour cream

Chocolate Ganache<e/m>
12-oz dark or semisweet chocolate chips
1/2 tsp vanilla extract
1 cup heavy cream

Cheesecake Filling
1/4 cup butter, room temperature
8-oz cream cheese, room temperature
2 tsp vanilla bean paste (or 1 tsp vanilla extract)
1 cup confectioners’ sugar
pinch salt

Make the cupcakesPreheat oven to 350F. Line a 12-cup muffin pan with paper liners.
In a medium bowl, sift together flour, cocoa powder, baking powder and salt.
In a large bowl, cream together butter and sugar until light. Beat in eggs, one at a time, followed by vanilla extract. Stir in half of the flour mixture, followed by the sour cream. Stir in the remaining flour until mixture is uniform. Divide evenly into prepared paper liners.
Bake for 19-22 minutes, or until cupcakes are set and a toothpick inserted into the center comes out with only a few moist crumbs attached.
Turn cupcakes out onto a wire rack to cool completely.

Make the ganacheIn a large bowl, combine chocolate chips and vanilla extract. In a small pot or microwave-safe measuring cup, bring heavy cream to a boil, then pour over chocolate. Allow mixture to sit for 1 minute, then slowly stir using a spatula until a smooth ganache forms. Set aside to cool for at least 30-45 minutes, until thickened enough to pipe.

Make the cheesecake filling. In a medium bowl, beat together butter, cream cheese and vanilla until smooth. Blend in confectioners’ sugar and salt until uniform. Set aside.

Assemble: Using the cone method, insert a paring knife into the top of each cupcake and remove a cone of cake to create a cavity to fill. Cut off the base of the cone and save the “lid”. Fill cupcakes with cheesecake filling and replace the “lid” of the cupcake.
Transfer cooled ganache to a piping bag and pipe a generous swirl of ganache on top of each cupcake. Decorate with sprinkles and serve.

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