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.

What Makes These Fudge Cupcakes Perfect
- Simple Preparation: 2 bowls and 1 whisk required for the cupcakes
- Fool-Proof Recipe: easy to follow instructions for a 2-ingredient chocolate frosting
- The BEST texture and flavor: moist, fluffy, and rich chocolate cupcake base
- Addicting special touch: safe-to-eat cookie dough with steps for heat-treating flour

Dark Chocolate Cupcakes Ingredients
All Purpose Flour: You’ll need simple, plain, and classic all purpose flour for these cupcakes. Ensure you measure the flour properly to make sure you do not end up with hard, dry cupcakes.
Dark Chocolate Cocoa Powder: This is one of the most important ingredients in these cupcakes, as it provides the chocolate flavor and GREATLY impacts the structure of these cupcakes. If there is one thing you read, please note that this recipe calls for Dutch-processed cocoa powder. If you use regular cocoa powder, your cupcakes will not rise properly due to the chemical interactions between the cocoa powder and baking soda. I use the Hershey brand.
Baking Soda: You’ll only need baking soda to help these cupcakes rise and become light and fluffy. Baking powder and soda are completely different, so do not interchange baking soda with baking powder.
Salt: There may only be a small amount of salt in the grand scheme of things, but it is mighty in power. Salt brings out the chocolate flavor and enhances the sweetness in these cupcakes.
Sour Cream: Sour cream makes the cupcake moister and more tender. It can be substituted for Greek yogurt. However, ensure that the sour cream or greek yogurt is at room temperature.
Granulated Sugar: Simple, plain granulated sugar contributes to sweetness, moisture, and structure of these cupcakes.
Eggs: You'll need 2 large eggs at room temperature. If you forget to leave them out ahead of time, put them in a bowl of hot water for about 5 minutes before using.
Vegetable Oil: Vegetable oil is the best in cupcakes, as it creates a moister cupcake. You can substitute vegetable oil for any unflavored oil.
Pure Vanilla Extract: Pure vanilla extract rounds out the flavor in these cupcakes.
Buttermilk: Buttermilk creates a lighter, fluffier, more tender crumb. Do not substitute buttermilk for regular milk, as the structure and texture of these cupcakes will dramatically change.
Boiling Water: Boiling water reacts with the cocoa powder to create a deeper, richer chocolate flavor. The extra few minutes of effort are beyond worth it... I promise!

Heat-Treating Flour
Heat- treating flour is the process of heating flour in order to kill off harmful bacteria. You can heat treat flour in one of two ways:
- Oven: Preheat your oven to 350 degrees Fahrenheit. Sprinkle flour evenly and thinly across a sheet pan. Once the oven has preheated, cook the flour for about 10 minutes. Stir the flour every few minutes to ensure the flour heats evenly. If you have a food thermometer, the temperature of the flour needs to reach 160 degrees Fahrenheit. If you do not, keep an eye for the flour, as it should look stiff and slightly darker in color.
- Microwave: In a medium, microwave-safe bowl, heat the flour in 45 second intervals, stirring in between each round in the microwave to ensure the flour heats evenly. This should take between 3-5 rounds depending on the bowl you use and the strength of your microwave. The flour needs to reach 160 degrees Fahrenheit.

Assembling Cookie Dough Cupcakes
*PLEASE SEE MORE DETAILED INSTRUCTIONS IN RECIPE CARD BELOW*
Step 1: To begin, prepare the ganache frosting. You'll heat heavy whipping cream over medium heat and pour it over a bowl of chocolate chips. The important part about this is to make sure all chocolate chips are submerged in the heavy cream. Let the mixture sit for 2-3 minutes before using a whisk, starting in the center, to whisk the melted chocolate chips and heavy cream together.
Step 2: Next, cover the bowl of ganache with a piece of cling wrap and place the bowl in the fridge until after the cupcakes are assembled. The ganache should stay in the fridge for at least 1 hour.
Step 3: Preheat your oven and line your cupcake tin with liners. Prepare dark chocolate cupcakes by whisking dry ingredients and wet ingredients separately. Then, alternate adding dry ingredients and boiling water to the wet ingredients, whisking in between each addition.
Step 4: After preparing the batter, divide it between your liners and bake for 18-23 minutes until the cupcakes spring back when poked in the center with your pointer finger. A toothpick inserted into the center should come out with moist crumbs. Allow the cupcakes to cool for at least 15 minutes while you prepare the edible cookie dough.
Step 5: Meanwhile, while the cupcakes are cooling, heat-treat flour in the microwave or oven. Read "Heat-Treating Flour" above for more information. Prepare edible cookie dough by creaming butter and sugars, milk, and vanilla extract together. Add salt, cooled heat-treated flour, and mini chocolate chips to the batter. Once the cookie dough is prepared, roll 12 tablespoon-sized balls. Then, roll the remaining dough into smaller balls of various sizes for decoration.
Step 6: Next, use a teaspoon, small spoon, or coring tool to remove a portion of each cupcake's center. Place tablespoon-sized balls in each cupcake's center.
Step 7: Remove ganache from the fridge. Whip the ganache with an electric mixer on medium/high speed for 2-4 minutes or until the ganache is lighter in color and velvety in texture. If desired, place the frosting in a piping bag fitted with the tip of your choice. I use a Wilton 1M.
Step 8: Frost cupcakes with ganache and top with remaining cookie dough balls for decoration.
Step 9: After decorating, store at room temperature in an airtight container for up to one day before moving them to the fridge for the next 3 days due to the heavy whipping cream.

FAQ
These chocolate cupcakes are naturally moist as ever due to vegetable oil, sour cream, and buttermilk. However, to ensure your cupcakes come out moist and fluffy, measure your flour properly. This means either using a kitchen scale or spooning the flour into your measuring cups before leveling off the tops with a knife. Also, do not overbake cupcakes. Bake only until a toothpick comes out with moist crumbs, the centers are set, and the top of the cupcake springs back when you poke it with your pointer finger.
I do not recommend baking this cookie dough- both alone or in the cupcake. This cookie dough does not have any leavening agents (baking powder or baking soda), and it does not have the right ratio of ingredients for proper cookies, so it will not yield desirable results.
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Related Recipes
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Cookie Dough Fudge Cupcakes
- 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
Description
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!
Ingredients
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
- ⅓ cup (27g) dark cocoa powder, sifted
- 1 teaspoon (6g) baking soda
- ½ teaspoon (4g) salt
- ⅓ cup (75g)vegetable oil
- ¼ cup (65g) sour cream, room temperature
- ¾ cup (170g) granulated sugar
- 2 large eggs (100g), room temperature
- 1 teaspoon (4g) vanilla extract
- ⅔ cup (160g) buttermilk, room temperature
- ⅓ cup (75g) boiling water
For the Edible Cookie Dough
- ½ cup (110g) unsalted butter, room temperature
- ½ cup (120g) light brown sugar
- ⅓ cup (75g) granulated sugar
- 3 tablespoons (45g) milk
- 1 teaspoon (4g) vanilla extract
- 1 ½ cup all purpose flour (210g), heat treated then sifted
- ¼ teaspoon (2g) salt
- ½ cup (98g) mini chocolate chips
Instructions
For the Ganache Frosting
- Place dark chocolate chips in a medium, heat-proof bowl.
- 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.
- 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.
- 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.
- 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
- Preheat your oven to 325 degrees Fahrenheit, and line a 12-muffin tin with liners.
- In a medium-sized bowl, whisk all purpose flour, sifted dark cocoa powder, baking soda, and salt until combined.
- In a large bowl, whisk vegetable oil, room temperature sour cream, granulated sugar, room temperature eggs, vanilla extract, and buttermilk until fully combined.
- Bring water to a boil in a small saucepan over medium heat.
- Alternate adding the dry ingredients and boiling water, starting and ending with the dry ingredients. To do this, add ½ of the dry ingredients to the wet ingredients, and whisk for about 5 seconds before adding ½ of the boiling water. Whisk in ½ of the remaining dry ingredients to the batter before adding the remaining ½ 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.
- Divide batter between the 12 cupcake cavities- about ¼ cup and ⅓ cup of batter. The batter should almost fill the liners.
- 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.
- Let cupcakes cool for about 15 minutes before filling and frosting.
For the Edible Cookie Dough
- 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.
- 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.
- Mix milk and vanilla extract into the batter until smooth.
- Sprinkle salt into the batter before adding sifted, heat-treated flour. Mix until smooth and fully combined.
- Add chocolate chips or other desired mix-ins into the batter and mix until incorporated.
- Use a teaspoon, small spoon, or coring tool to remove a portion of the center of each cupcake.
- Roll cookie dough into about 1 tablespoon-sized balls. Stick one ball in each cupcake.
- Roll remaining cookie dough into small balls of various sizes to use as decoration on the cupcakes.
Frosting and Assembling
- 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.
- 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
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