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Cookie Dough Fudge Cupcakes

  • Author: Elise
  • Prep Time: 1 hour
  • Cook Time: 20 minutes
  • Total Time: 1 hour, 20 minutes
  • Yield: 12 cupcakes 1x
  • Category: Cupcakes, Chocolate, Chocolate Cupcakes, Dark Chocolate, Cookie Dough
  • Method: Bake
  • Cuisine: American


These Chocolate Ganache Cookie Dough Cupcakes are simply a dream. They have a dark chocolate cupcake base filled with edible chocolate chip cookie dough and are topped with a whipped ganache frosting and additional cookie dough pieces. They will be the most indulgent and rich cupcakes you will ever serve!



For the Ganache Frosting 

  • 2 cups (350g) dark chocolate chips
  • 1 cup (240g) heavy whipping cream

For the Dark Chocolate Cupcakes

  • 1 cup (140g) all purpose flour
  • 1/3 cup (27g) dark cocoa powder, sifted
  • 1 teaspoon (6g) baking soda
  • 1/2 teaspoon (4g) salt
  • 1/3 cup (75g)vegetable oil
  • 1/4 cup (65g) sour cream, room temperature
  • 3/4 cup (170g) granulated sugar
  • 2 large eggs (100g), room temperature
  • 1 teaspoon (4g) vanilla extract
  • 2/3 cup (160g) buttermilk, room temperature
  • 1/3 cup (75g) boiling water

For the Edible Cookie Dough

  • 1/2 cup (110g) unsalted butter, room temperature
  • 1/2 cup (120g) light brown sugar
  • 1/3 cup (75g) granulated sugar
  • 3 tablespoons (45g) milk
  • 1 teaspoon (4g) vanilla extract
  • 1 1/2 cup all purpose flour (210g), heat treated then sifted
  • 1/4 teaspoon (2g) salt
  • 1/2 cup (98g) mini chocolate chips


For the Ganache Frosting 

  1. Place dark chocolate chips in a medium, heat-proof bowl.
  2. In a medium-sized saucepan over medium heat, heat heavy whipping cream until it begins to simmer. The mixture should begin to bubble throughout, and you should see steam coming from it. Do not let the cream fully boil.
  3. Immediately pour the cream over your chocolate chips. Push chocolate chips under the cream if they aren’t fully covered by the heavy cream. You do not want any chocolate chips exposed.
  4. Let the mixture sit for 2-3 minutes, uncovered, before using a rubber spatula or wire whisk to combine. Start by making small circles in the center of the bowl. Continue making a swirl motion and slowly begin working outside the center of the bowl as the mixture combines.
  5. Place a piece of cling wrap directly on top of the ganache. Place the larger bowl in the fridge until later. If storing for longer than 2 hours, you will need to remove the ganache and let it sit at room temperature prior to whipping.

For the Dark Chocolate Cupcakes 

  1. Preheat your oven to 325 degrees Fahrenheit, and line a 12-muffin tin with liners.
  2. In a medium-sized bowl, whisk all purpose flour, sifted dark cocoa powder, baking soda, and salt until combined.
  3. In a large bowl, whisk vegetable oil, room temperature sour cream, granulated sugar, room temperature eggs, vanilla extract, and buttermilk until fully combined.
  4. Bring water to a boil in a small saucepan over medium heat.
  5. Alternate adding the dry ingredients and boiling water, starting and ending with the dry ingredients. To do this, add 1/2 of the dry ingredients to the wet ingredients, and whisk for about 5 seconds before adding 1/2 of the boiling water. Whisk in 1/2 of the remaining dry ingredients to the batter before adding the remaining 1/2 of the boiling water. Add final portion of dry ingredients to the batter, and mix until the dry ingredients are just incorporated. Batter will be very thin and will not be completely smooth, but continue mixing until any major lumps have disappeared.
  6. Divide batter between the 12 cupcake cavities- about 1/4 cup and 1/3 cup of batter. The batter should almost fill the liners.
  7. Bake cupcakes for 18-23 minutes. If you have an uneven oven, turn your tin at the 17 minute mark, as turning earlier will risk deflating the cupcakes. Cupcakes should bounce back when poked in the center, and a toothpick inserted into the center will come out with just a few crumbs.
  8. Let cupcakes cool for about 15 minutes before filling and frosting.

For the Edible Cookie Dough 

  1. Heat treat your flour in the microwave in 45 second increments, stirring between each round or in the oven, stirring the flour every few minutes for about 10 minutes. The temperature of the flour should reach 165 degrees Fahrenheit throughout. Let flour cool for at least 10 minutes before sifting and using. Read “Heat-Treating Flour” section above for more tips on heat treating.
  2. In a large bowl or in the bowl of your stand mixer, beat room temperature butter, granulated sugar, and light brown sugar until smooth and creamy. This should be between 2-3 minutes.
  3. Mix milk and vanilla extract into the batter until smooth.
  4. Sprinkle salt into the batter before adding sifted, heat-treated flour. Mix until smooth and fully combined.
  5. Add chocolate chips or other desired mix-ins into the batter and mix until incorporated.
  6. Use a teaspoon, small spoon, or coring tool to remove a portion of the center of each cupcake. 
  7. Roll cookie dough into about 1 tablespoon-sized balls. Stick one ball in each cupcake.
  8. Roll remaining cookie dough into small balls of various sizes to use as decoration on the cupcakes.

Frosting and Assembling 

  1. Remove the ganache from the fridge. Use a handheld electric mixer or stand mixer with the whisk attachment to beat the ganache for 3-5 minutes until the ganache has turned lighter in color, smooth, and airy in texture.
  2. If desired, transfer whipped ganache to a piping bag fitted with a star (or any) tip. Frost the cupcakes and decorate with remaining cookie dough balls. Store cupcakes covered at room temperature for 1 day before transferring to the fridge for up to 3 days due to the heavy whipping cream.

Keywords: Cookie Dough, Edible Cookie Dough, Cookie Dough Cupcakes, Dark Chocolate Cupcakes, Ganache Frosting