These moist and fluffy cookie dough cupcakes are studded with mini chocolate chips and filled with decadent pockets of raw cookie dough. After baking they are frosted with a generous swirl of sweet cookie dough frosting, and garnished with even more cookie dough pieces. Yes, you read that right, triple the cookie dough flavor in one single bite! If you are a cookie dough lover, you do not want to miss out on these cupcakes!

A cookie dough cupcake cut in half to show the cookie dough inside.
There’s real cookie dough flavor in every bite!

To be honest I made this recipe only because I wanted to make sure that my cookie dough frosting had the perfect counterpart. Also because hello, it’s cookie dough!

It was also important to me that the cookie dough was baked into the recipe instead of having to core and stuff them afterwards. I didnt want to deal with an extra step and thought it was so much easier this way.

The base of this cupcake is made from the recipe for my fluffy chocolate chip cupcakes but to make it even better, it’s stuffed with homemade cookie dough right into the batter. Don’t be scared to make your own cookie dough, it’s super easy and safe to eat using heat treated flour- I’ll show you how to do it below!

As a trained pastry chef I am excited to share this recipe with you because not only can you make these delicious cupcakes, but now you can also make a small batch of cookie dough on those days when you just *need it*.

If that wasnt enough flavor for you, you then have the option to frost them with the cookie dough frosting that I mentioned above, or if you’d like you can try this chocolate buttercream frosting or whipped cream cheese frosting!

Excited as I am to get started? Grab your flour and a baking sheet and let’s get started!

Heat treated Flour

Heat treated flour is just heating the flour in a microwave or an oven to kill the bacteria that raw flour can have.

Have you always been told that you shouldn’t eat cookie dough because of the eggs? That’s not what I would be worried about at all, especially with pasteurized eggs these days. It’s more so that you kill the salmonella that could be hiding in your raw flour.

All purpose flour spread all over a baking sheet lined with parchment paper.
Keep the flour on the parchment to easily move it into a bowl.

There’s 2 ways to heat treat flour:

  1. In the microwave. Add the flour to a microwaveable safe bowl and heat on high for 30 seconds. Stir, then heat again for another 30 seconds and your’e done.
  2. Preheat the oven to 350° F and line a baking sheet with parchment paper. Spread the flour on the parchment paper and bake for 5 minutes. If you are making the cupcakes right after this then leave the oven on.

In both circumstances you want to make sure the flour has totally cooled before adding the rest of the ingredients in the recipe. Otherwise it can melt the chocolate chips- I totally made this mistake, so I am speaking from experience here.

Make the cookie dough

It’s super easy to make safe to eat cookie dough! You need simple ingredients like:

  • cooled heat treated flour
  • softened butter
  • powdered sugar
  • granulated sugar
  • vanilla
  • milk or cream
  • salt
  • mini chocolate chips

All you have to do is cream the butter with the two sugars until light and fluffy. We’re using a mix of powdered and granulated sugar here so that the texture of the cookie dough is fluffy but stays uniform. The powdered sugar helps to keep it together and create that soft melt in your mouth texture.

Next add the rest of the ingredients and mix until combined, that’s it. If you used your stand mixer, you’ll need to wash it out to make the cupcake batter.

I recommend using mini chocolate chips because regular ones are too big to roll the cookie dough into small balls. If you don’t have mini chocolate chips you can rough chop the regular sized ones or a chocolate bar.

Chilling the cookie dough

After making, put the cookie dough in the fridge or freezer to chill for at least 20 minutes. Because we are baking the dough inside the cupcakes this is a crucial step to make sure the batter stays in its shape and doesn’t melt.

If you skip the chilling part the cookie dough will spread throughout the batter. Good thing is that now it’s time to make the cupcakes, so you can let the cookie dough do its thing in the fridge while you prep them.

Make the cupcake batter

I like to use cake flour in a lot of my homemade cupcake recipes because it is lighter than all purpose flour and helps the cupcakes come out fluffier.

  • Prep for baking: If not already heated from making the heat treated flour, preheat the oven to 350° F and line a 12 cup muffin tin with cupcake liners.
  • Combine the dry ingredients: In a small bowl add the flour, baking powder, baking soda and salt and set aside.
  • Cream the butter and sugar: In a mixing bowl or in a the bowl of a hand mixer, cream the butter for 1 minute, then add the sugar and cream again until fluffy
  • Add eggs and flavor: Next add the eggs, egg whites, and vanilla while the mixer is running on low. Then move up to medium speed to incorporate.
  • Alternate ingredients: Alternate adding the dry and wet ingredients, starting and ending with the dry.
  • Chocolate chips: Lightly dust the mini chocolate chips with flour and stir them into the batter with a spatula.
  • Prep the cookie dough: Now that the cookie dough has cooled, take a teaspoon sized amount and roll it into a ball. Repeat making at least 12.
  • Fill the liners– Fill the cupcake liners halfway with cupcake batter, then drop a cookie dough ball into the center. Cover the dough with more cupcake batter until it reaches 3/4 of the way up.
  • Bake- Bake the cupcakes for 18-19 minutes, then remove and cool completely on a wire rack.

Frosting and decorating

Frost the cupcakes with cookie dough frosting. If you want to pipe the frosting you need to use a wide open round tip that is large enough to have the chocolate chips pipe through. The Ateco 809 tip is what I use to pipe onto my cupcakes.

You can also use an offset spatula or even an ice cream scoop to frost the cupcakes.

To garnish, make some more small cookie dough balls with the left over cookie dough and top the frosting with them.

A cookie dough cupcake frosted with cookie dough garnish on an over turned plate.
Top with cookie dough frosting and the remaining cookie dough to add garnish.

Yield and storage

This recipe makes 12 cupcakes. The cookie dough makes enough to fill each cupcake plus have extra to turn into garnish.

Storing– there is no need to store the cupcakes in the fridge. Keep them in an airtight container at room temperature for up to 5 days.

Freezing– I recommend freezing these cupcakes without the frosting. Then once defrosted, make and top the cupcakes with the icing. Place the cupcakes in an air tight zip top bag squeezing out as much air as possible. Freeze for up to 2 months.

A cookie dough cupcake frosted with cookie dough garnish on an over turned plate.
5 stars (1 rating)

Easy Stuffed Cookie Dough Cupcakes

These moist and fluffy cookie dough cupcakes are studded with mini chocolate chips and filled with decadent pockets of raw cookie dough. After baking they are frosted with a generous swirl of sweet cookie dough frosting, and garnished with even more cookie dough pieces. Yes, you read that right, triple the cookie dough flavor in one single bite! If you are a cookie dough lover, you do not want to miss out on these cupcakes!

Ingredients

Cookie dough

  • 3/4 cup all purpose flour, sifted
  • 1/4 cup unsalted butter, softened
  • 2 tbsp powdered sugar
  • 2 tbsp granulated white sugar
  • 1/2 tsp vanilla extract
  • 2 tsp milk
  • 1 pinch kosher salt
  • 1-2 tbsp mini chocolate chips

Cupcakes

  • 1 3/4 cup cake flour, + 2 tsp divided
  • 1 tsp baking powder
  • 1/4 tsp baking soda
  • 1/4 tsp kosher salt
  • 1/2 cup unsalted butter, softened
  • 1 cup granulated sugar
  • 1 egg, large
  • 2 egg whites, large
  • 2 tsp vanilla extract
  • 1/2 cup buttermilk, room temperature
  • 1 cup mini chocolate chips

Instructions
 

Make the cookie dough

  • All purpose flour spread all over a baking sheet lined with parchment paper.
    Preheat the oven to 350°F and line a rimmed baking sheet with parchment paper. Spread the 3/4 cup flour in an even layer and bake for 5 minutes then set aside to cool.
  • Creamed butter, powdered sugar and granulated sugar in a mixing bowl with a paddle attachment.
    In the bowl of a hand or stand mixer fitted with the paddle attachment, or in a small bowl with a whisk, cream the 1/4 cup butter with the 2 tbsp powdered sugar and 2 tbsp granulated sugar until its light and fluffy about 1 minute.
  • Raw cookie dough mixed in a mixing bowl.
    Add in the 1/2 tsp vanilla extract and the 2 tsp milk and mix lightly. Add in the 3/4 cup cooled heat treated flour, pinch of salt, and the mini chocolate chips. Mix well and place in the fridge for 20 minutes.

Make the cupcakes

  • Line a muffin tin with 12 cupcake liners and set aside.
  • In a medium size bowl combine the 1 and ¾ cup cake flour, 1 tsp baking powder, ¼ tsp baking soda, and ¼ tsp kosher salt. Whisk until combined and set aside.
  • Creamed butter and sugar in a mixing bowl.
    In the bowl of a hand mixer or stand mixer fitted with the paddle attachment, cream the ½ cup butter for 1 minute on medium speed. Scrape down the bowl and add 1 cup sugar. Mix on medium speed for 2 minutes until light and fluffy.
  • Scrape down the bowl and add the egg, 2 egg whites and 2 tsp vanilla extract. Mix for 1 minute on medium speed.
  • With the mixer on low speed, add in 1/3rd of the dry ingredients, mix, then add half of the buttermilk and alternate (mixing in between) ending with the dry ingredients. Mix only until combined. Do not overmix.
  • Cookie dough cupcake batter in a mixing bowl.
    In a small bowl combine the 1 cup mini chocolate chips and remaining 2 tsp flour. Mix to coat the chocolate chips evenly. Pour the chocolate chips into the batter and mix lightly by hand.
  • Halfway filled cupcake liners with batter.
    Using a cookie scoop, scoop batter halfway up in a muffin liner.
  • Remove the cookie dough from the fridge and using a teaspoon, scoop at least 12 small balls. Drop each one into the center of the batter then top with more batter until it reaches 3/4 of the way full. Its ok if its a little more!
  • Cupcake batter in a 12 cup muffin tin.
    Bake for 18-19 minutes, then remove and cool completely on a wire rack.
  • A cookie dough cupcake frosted with cookie dough garnish on an over turned plate.
    When the cupcakes are cooled frost them with cookie dough frosting.
  • Optional– To garnish- scoop more cookie dough and add to the top of frosted cupcakes.

Notes

You can also frost these with chocolate buttercream frosting. 
Serving: 1cupcake, Calories: 372kcal, Carbohydrates: 51g, Protein: 5g, Fat: 16g, Saturated Fat: 10g, Polyunsaturated Fat: 1g, Monounsaturated Fat: 3g, Trans Fat: 0.5g, Cholesterol: 48mg, Sodium: 148mg, Potassium: 60mg, Fiber: 1g, Sugar: 31g, Vitamin A: 429IU, Vitamin C: 0.1mg, Calcium: 61mg, Iron: 1mg
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