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Chocolate Cheesecake Cupcakes with Whipped Ganache Frosting

Course Cupcakes, Dessert
Cuisine American
Keyword chocolate cheesecake cupcakes, cupcakes
Prep Time 15 minutes
Cook Time 28 minutes
Total Time 43 minutes
Servings 24 cupcakes
Calories 339kcal
Author Trish - Mom On Timeout


Cheesecake Filling

  • 8 oz Philadelphia Cream Cheese
  • 1 egg room temperature
  • 1/8 tsp salt
  • 1/3 cup sugar
  • 1 tbsp lemon juice


  • 1 1/3 cups sugar
  • 8 tbsp unsalted butter softened
  • 2 eggs room temperature
  • 2 tsp vanilla
  • 1 1/3 cups flour
  • 1/2 cup baking cocoa
  • 1/2 tsp baking soda
  • 1/2 tsp salt
  • 1 tsp baking powder
  • 1 cup buttermilk

Whipped Ganache Frosting

  • 8 oz semi sweet chocolate chips
  • 8 oz bitter sweet chocolate chips
  • 2 cups heavy whipping cream 1 pint


  • Preheat oven to 325F.
  • Line 2 muffin tins with cupcake liners and set aside.

Cheesecake Filling

  • Beat the cream cheese until light and fluff. Mix in the egg, beating until well combined. Beat in the remaining ingredients, scraping down the mixer bowl as necessary. Set the filling to the side.


  • Cream butter and sugar in a mixer until light and fluffy. Add in the eggs, one a time, beating well after each addition. Beat in vanilla.
  • Whisk together the flour, cocoa, baking soda, salt, and baking powder in a medium bowl.
  • Add to the butter and sugar mixture alternating with the buttermilk Beat well after each addition.
  • Fill liners about 1/3 full. Spoon in one tablespoon of the cheesecake mixture. Top with enough cupcake batter to fill just to 2/3 full.
  • Bake for 25-28 minutes or until the top of the cupcake springs back when pressed on gently. Let cupcakes cool completely before frosting. Note: The top will sink slightly as the cheesecake settles.

Ganache Frosting

  • Coarsely chop the chocolate chips. This helps them to melt better.
  • Heat the heavy whipping cream in the microwave, in a microwave safe container on high, in 30 second increments until cream is just beginning to simmer.
  • Pour the cream over the chocolate and stir gently to make sure that all of the chocolate is covered with the hot cream. Let sit for 2-3 minutes.
  • Gently whisk the cream and chocolate together until the chocolate has completely melted and the mixture is smooth and homogeneous. Let the ganache cool to room temperature (at least two hours).
  • Whisk the ganache with a stand mixer for several minutes until frosting meets your desired consistency.
  • Pipe or spread onto the cooled cupcakes.


Recipe adapted from All-Star Chocolate Cupcakes.


Calories: 339kcal | Carbohydrates: 32g | Protein: 4g | Fat: 22g | Saturated Fat: 14g | Cholesterol: 70mg | Sodium: 155mg | Potassium: 218mg | Fiber: 2g | Sugar: 21g | Vitamin A: 588IU | Vitamin C: 1mg | Calcium: 85mg | Iron: 1mg