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Chocolate filled cupcakes on a cooling rack with its wrapper undone

Chocolate Filled Cupcakes with Ganache Filling

These decadent and moist chocolate cupcakes are filled with a creamy chocolate ganache filling and topped with chocolate buttercream. They are a chocolate lover's dream!
5 from 3 votes
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Course: Cupcakes
Cuisine: American
Diet: Kosher
Keyword: chocolate filled cupcakes, cupcake filling, ganache filled cupcakes, how to fill a cupcake
Prep Time: 15 minutes
Cook Time: 18 minutes
cooling time: 20 minutes
Total Time: 1 hour 3 minutes
Servings: 12 cupcakes
Calories: 154kcal
Author: Sam Adler


Chocolate Cupcakes

  • 3/4 cup granulated sugar
  • 2/3 cup all purpose flour
  • 1/3 cup cocoa powder
  • 1/2 tsp baking soda
  • 1/4 tsp baking powder
  • 1/4 tsp kosher salt
  • 1 egg large
  • 1/2 tsp vanilla extract
  • 1/3 cup whole milk yogurt
  • 1/3 cup black coffee warm or cold
  • 1/8 cup vegetable oil

Chocolate Ganache Filling

  • 4 oz chopped chocolate semi sweet
  • 1/4 cup heavy cream


Make the cupcakes

  • Preheat the oven to 350° F and line a 12 cup muffin tin with cupcake liners, set aside.
  • In a bowl of a hand or stand mixer fitted with the paddle attachment, combine the 3/4 cup sugar, 2/3 cup flour, 1/3 cup cocoa, 1/2 tsp baking soda, 1/4 tsp baking powder, and 1/4 tsp kosher salt. Whisk lightly or mix on low to combine.
  • Add the 1 egg, 1/2 tsp vanilla extract 1/3 cup whole milk yogurt, 1/3 cup black coffee, and 1/8 cup vegetable oil and mix on low speed working up to medium as it combines. Mix for 2 minutes on medium speed.
  • Fill the cupcake liners 2/3rd of the way full. Bake for 18 minutes or until the tops of the cupcakes bounce back when lightly pressed.

Make the chocolate ganache filling

  • In a small bowl, add the 4 oz chopped chocolate. Heat the cream in the microwave for 15-30 seconds at a time until scalding. Pour the cream over the chocolate and let sit for 5 minutes. DO NOT stir right away. Stir with a spatula after 5 mins until smooth.
  • Refrigerate the ganache for 20 minutes to harden.

Fill the cupcakes

  • Use a cupcake corer or a small knife, cut a 1/2 inch deep hole about the size of a quarter and lift the top off, saving it for after.
  • Fill the cupcake using a teaspoon of ganache and place the top of the cupcake back on. Press lightly, then top with buttercream frosting! (See notes below for frosting recipe)


Here's my chocolate buttercream recipe to use to top the cupcakes. 
Make sure to only fill the cupcake liners 2/3 of the way full. If you fill them too high they will overflow and you may not have enough to make 12 cupcakes. 


Nutrition Facts
Chocolate Filled Cupcakes with Ganache Filling
Amount Per Serving (1 cupcake)
Calories 154 Calories from Fat 54
% Daily Value*
Fat 6g9%
Saturated Fat 4g25%
Trans Fat 1g
Polyunsaturated Fat 1g
Monounsaturated Fat 2g
Cholesterol 21mg7%
Sodium 116mg5%
Potassium 94mg3%
Carbohydrates 25g8%
Fiber 2g8%
Sugar 18g20%
Protein 2g4%
Vitamin A 99IU2%
Vitamin C 1mg1%
Calcium 25mg3%
Iron 1mg6%
* Percent Daily Values are based on a 2000 calorie diet.