Molten Cookie Dough Cupcakes

Talk about indulgence! These molten cookie dough cupcakes are homemade vanilla cupcakes filled with cookie dough and topped with chocolate chip cookie dough buttercream. Here I’ll teach you how to make safe-to-eat cookie dough with success tips from the talented Kristen Tomlan, founder of NYC.

molten chocolate chip cookie dough cupcakes

Today’s new cupcake recipe comes straight from the brilliant and sweet-as-ever owner of DŌ Cookie Dough Confections, Kristen Tomlan. Kristen has become one of my dearest friends over the years– the power of cookies literally connected us! She’s a gracious, hardworking, and business-owning woman from whom I gather so much inspiration. Kristen just released her cookbook debut, surely to hit the best-selling list, and I couldn’t be more excited for her. (Let’s all give a WOOHOO for Kristen!) She is generously allowing me to share her cookbook with all of you and publish one of the best recipes found inside.

Ok, every recipe of hers is the best, but I had to play favorites with this one because she based her molten cookie dough cupcakes off of my vanilla cupcakes recipe. ♥

Hello, Cookie Dough by Kristen Tomlan

Hello, Cookie Dough by Kristen Tomlan is a dessert lovers dream come true. This book is a visual masterpiece with pictures on every single page. It offers a must-have collection of 110 delicious dessert recipes that bakers of any skill level want need. Filled with dozens of safe-to-eat cookie dough recipes and flavors, plus endless chapters of sweet treats including brownies, cakes, cookies, fudge, and breakfast sweets all centered around our favorite flavor: cookie dough! Kristen shares her incredible story of how she launched her brand, literally fought to save her life, plus hundreds of kitchen tips and recipe success secrets.

This is so much more than a cookbook; it’s a huge resource of recipes, a fun gift, and a gorgeous coffee table book (that you’ll READ and USE).

Order: Amazon

Hello Cookie Dough cookbook by Kristen Tomlan

chocolate chip cookie dough cupcake

3 Parts to Molten Cookie Dough Cupcakes

  1. Vanilla Cupcakes
  2. Molten Cookie Dough Center
  3. Cookie Dough Buttercream

Heat-Treated Flour + Pasteurized Egg Whites

Kristen’s molten cookie dough cupcakes (and all of her cookie dough and dessert recipes) are completely safe to eat because we’re using heat-treated flour and pasteurized egg whites. The unique aspect about her cookie dough is that you can eat it raw and it tastes just like cookie dough because IT IS cookie dough– and without any substituted ingredients. Another unique aspect about Kristen’s dough recipes is that you can bake them, too. Yes, her cookie dough recipes are bake-able for actual baked cookies.

  1. Flour: Raw flour can be a carrier of E. coli unless it goes through a heating process to kill the bacteria. (Think about it– flour is usually baked in a recipe.) You can purchase heat-treated flour from her shop! Or scroll below to find her homemade instructions. It’s easy!
  2. Eggs: Kristen uses and recommends using only egg whites in most of her cookie dough recipes. (As the creator of the original edible cookie dough bakery, I would trust her word!!) You can purchase pasteurized egg whites in a carton at most major grocery stores. A great brand to look for is AllWhites. Do not purchase products with egg whites and yolks combined, as those are not recommended for Kristen’s dough recipes. Or you can pasteurize the egg whites yourself– lots of easy tutorials available if you give it a quick search online! If you’d rather not use egg whites, substitute 2 Tablespoons cornstarch whisked with 1/3 cup room temperature milk. Whole milk is best, but 2% or even nondairy milks work too.

heat treated flour for cookie dough

How to Make Cookie Dough Cupcakes

  1. Make edible cookie dough: We’ll use this cookie dough as the filling of the cupcakes as well as in the buttercream frosting. This is Kristen’s signature chocolate chip cookie dough that you get from her famous bakery! Chill it for about 15 minutes before rolling into balls so it’s not as sticky.
  2. Roll into balls: Take 3/4 cup of cookie dough and roll into 12 1-Tablespoon balls. Set them aside in the refrigerator as you bake the cupcakes. These cookie dough balls will go inside our cupcakes. Set the remaining cookie dough aside for the frosting.
  3. Make the cupcakes: We’re using similar ingredients to my vanilla cupcakes. Kristen whisks the sour cream and milk together, then adds the mixture with the flour.
  4. Press cookie dough into cupcakes: Let the baked cupcakes cool for just 5 minutes. This is actually where I messed up my first time! I let the cupcakes cool completely, then had trouble pressing the  cookie dough ball inside. Pressing the cookie dough ball into a warm cupcake totally helps! Plus, the cookie dough slightly melts. Glorious.
  5. Make the frosting: I cover that next!

cookie dough cupcakes batter

I love that we don’t need to carve out a hole in the cupcake. Instead, literally press the cold cookie dough ball into the warm cupcake. The dough ball won’t sit completely flat, so expect a little lump on top. Don’t worry, you’ll cover it with frosting!

stuffing chocolate chip cookie dough inside cupcakes

Chocolate Chip Cookie Dough Buttercream

If cookie dough and buttercream joined forces, you’d literally have… heaven? Yes, that sounds right. Here we’re making a creamy vanilla buttercream and mixing in the cookie dough reserved from the cupcake’s filling.

I love that this buttercream is slightly salted, so it’s not overly sweet. By itself, it’s reminiscent of actual cookie dough. Use a spoon to break little chunks of the leftover cookie dough, then beat it into the frosting on low speed. It’s ok if the cookie dough chunks are not fully combined into the buttercream. (Because why wouldn’t you want surprise cookie dough bites in frosting?!)

You can spread the frosting onto the cupcakes with a knife or icing spatula or apply with a large round piping tip. The cookie dough chunks will get stuck in a smaller tip.

cookie dough buttercream frosting

cookie dough frosting

These Cookie Dough Cupcakes:

  • Are super soft, rich, & buttery
  • Surprise you with cookie dough inside
  • Are impressive, yet totally foolproof
  • Require a few steps, but are so very worth it 🙂

molten chocolate chip cookie dough cupcakes

cookie dough cupcakes

How to Heat Treat Flour

Option 1 – Microwave

  1. You can heat treat your entire bag of flour or just treat the amount you need in a single recipe. If you’re heating just enough for the recipe, add an extra 1/2 – 1 cup to be sure you have enough.
  2. Place the flour in a microwave-safe bowl and heat on high for 30 seconds at a time, stopping and stirring after each. Stir well to make sure none of the flour burns. Use an instant-read thermometer to test the flour in several places to make sure it has reached 165°F (74°C). If you get a lower reading in one area, stir and heat for an additional 30 seconds until it’s all ready.
  3. Measure the amount of flour you need and use in the recipe, then let it cool completely.

Option 2 – Oven

  1. Preheat oven to 300°F (149°C). Spread more flour than the recipe calls for on an un-greased rimmed baking pan, such as a 9×13 inch baking pan or 9×9 inch baking pan. Then follow a process similar to the microwave method by stirring and checking the temperature at 2 minute intervals. Be sure to check multiple spots of the flour to make sure it has all reached 165°F (74°C).
  2. If some flour sticks to the bottom or sides of the pan, don’t worry, just leave it there. You used more flour than needed in the recipe anyway. Don’t scrape it off because it will add small clumps to your batter/dough.
  3. If your flour is really clumpy, your oven might be too hot. Break it up with your fingers or pour all the flour into a bowl and whisk it. Discard any chunks if necessary.
  4. Measure the amount of flour you need and use in the recipe, then let it cool completely.
Print
chocolate chip cookie dough cupcake

Molten Cookie Dough Cupcakes

  • Author: Sally
  • Prep Time: 1 hour
  • Cook Time: 18 minutes
  • Total Time: 2 hours
  • Yield: 12 cupcakes
  • Category: Desserts
  • Method: Baking
  • Cuisine: American

Description

These molten cookie dough cupcakes are homemade vanilla cupcakes filled with cookie dough and topped with chocolate chip cookie dough buttercream. Review the recipe notes and information about safe-to-eat flour before beginning.


Ingredients

Cookie Dough

  • 2 and 1/4 cups (280g) heat-treated all-purpose flour* (spoon & leveled)
  • 2 and 1/4 teaspoons cornstarch
  • 3/4 teaspoon salt
  • 3/4 cup (12 Tbsp; 170g) unsalted butter, softened to room temperature
  • 1 cup (200g) packed light or dark brown sugar
  • 1/3 cup (80ml) pasteurized egg whites, at room temperature*
  • 2 teaspoons pure vanilla extract
  • 1 cup (180g) mini semi-sweet chocolate chips

Cupcakes

  • 1 and 3/4 cups (215g) all-purpose flour (spoon & leveled)
  • 1 teaspoon baking powder
  • 1/4 teaspoon baking soda
  • 1/2 teaspoon salt
  • 1/2 cup (120ml) whole milk, at room temperature
  • 1/2 cup (120g) sour cream, at room temperature
  • 1/2 cup (1 stick; 115g) unsalted butter, softened to room temperature
  • 1 cup (200g) granulated sugar
  • 1/3 cup (80ml) pasteurized egg whites, at room temperature*
  • 2 teaspoons pure vanilla extract

Cookie Dough Buttercream

  • 1 cup (2 sticks; 230g) unsalted butter, softened to room temperature
  • 2 teaspoons pure vanilla extract
  • 1 Tablespoon heavy cream or milk
  • 1 teaspoon salt
  • 3 cups (360g) confectioners’ sugar, sifted
  • optional garnish: reserved cookie dough, sprinkles, and/or chocolate chips

Instructions

  1. Make the cookie dough: In a medium bowl, whisk the heat-treated flour, cornstarch, and salt together. Set aside.
  2. Using a handheld or stand mixer fitted with the paddle attachment, beat the butter on medium speed in a large bowl until smooth and creamy, about 2 minutes. Add the brown sugar and mix on medium until light and fluffy, about 3 full minutes. Using a rubber spatula, scrape down the sides and up the bottom of the bowl as needed. Add the egg whites and vanilla extract and mix until fully incorporated, about 2 minutes.
  3. Add half of the flour mixture and mix on low just until the powdery texture of the flour disappears, about 15 seconds. Immediately add the rest of the flour mixture and mix until combined. Remove the bowl from the mixer and use a rubber spatula to fold in the chocolate chips.
  4. Freeze or refrigerate the cookie dough for 15 minutes or until the dough is easy to handle. Roll the dough into 12 one-Tablespoon-size balls, place on a plate lined with parchment paper, then refrigerate until step 9. Cover the remaining cookie dough and set aside at room temperature until step 11.
  5. Preheat the oven to 350°F (177°C). Line a 12-cup muffin pan with cupcake liners.
  6. Make the cupcakes: Whisk the flour, baking powder, baking soda, and salt together in a medium bowl. In a small bowl, whisk the milk and sour cream together until smooth. Set aside.
  7. Using a handheld or stand mixer fitted with the paddle attachment, beat the butter and sugar together on medium speed in a large bowl until light and fluffy, about 3 minutes. Using a rubber spatula, scrape down the sides and up the bottom of the bowl as needed. Add the egg whites and vanilla and beat for 2 minutes, or until the mixture is totally incorporated. With the mixer on low, alternate additions of the flour mixture and the sour cream mixture, starting and ending with flour. Beat for an additional 30 seconds or until the batter appears smooth and creamy.
  8. Fill cupcake liners about 3/4 full. Bake for 16-19 minutes or until the cupcake edges are golden brown and a toothpick inserted in the center comes out clean. Remove from the oven and let cool in the pan for 5 minutes.
  9. Remove cupcakes from the pan and carefully press 1 chilled cookie dough ball into the center of each cupcake. The dough ball might not sit completely flat, so expect a little lump on top. Don’t worry, you’ll cover it with frosting. Cool cupcakes completely.
  10. While the cupcakes cool, make the cookie dough buttercream: Using a handheld or stand mixer fitted with the paddle attachment, beat the butter in a large bowl on medium speed for 3 minutes, or until light, fluffy, and completely smooth. Add the vanilla extract, milk, and salt and beat until combined. Using a rubber spatula, scrape down the sides and up the bottom of the bowl as needed. Add the confectioners’ sugar, then beat on low speed for 15 seconds. Switch to medium-high speed and beat the frosting until super light and fluffy, about 4-5 minutes. The frosting will become lighter in color as air is whipped into it.
  11. Break the remaining cookie dough into quarter-size chunks. (If desired, save enough dough to make 12 little cookie dough balls as garnish on top!) With the mixer running on medium speed, add the cookie dough chunks. Mix just until incorporated– some chunks can remain.
  12. Once the cupcakes are completely cool, top with frosting. You can spread the frosting with a knife or icing spatula or apply with a large round piping tip. (The cookie dough chunks will get stuck in a smaller tip.) Decorate with garnishes, if desired.
  13. Leftover cupcakes keep well covered tightly in the refrigerator for 3 days.

Notes

  1. Make Ahead & Freezing Instructions: Plain cupcakes can be made ahead 1 day in advance, covered, filled with cookie dough balls, and stored in the refrigerator overnight. Buttercream can also be made 1 day in advance, covered, and stored in the refrigerator until ready to use. Bring cupcakes and buttercream to room temperature before frosting. Freeze frosted, unfrosted, filled, or unfilled cupcakes for up to 2-3 months. Thaw overnight in the refrigerator.
  2. Heat Treated Flour: See note/instructions above recipe or purchase it online.
  3. Pasteurized Egg Whites: You can purchase pasteurized egg whites in a carton at most major grocery stores. Check the dairy section or near where the eggs are sold. A great brand to look for is AllWhites. Do not purchase products with egg whites and yolks combined, as those are not recommended for Kristen’s dough recipes. Or you can pasteurize the egg whites yourself– lots of easy tutorials if you give it a quick search online! If you’d rather not use egg whites, substitute 2 Tablespoons cornstarch whisked with 1/3 cup room temperature milk. Whole milk is best, but 2% or even nondairy milks work too.
  4. Whole Milk & Sour Cream: Whole milk and sour cream are strongly recommended for the best taste and texture. A full fat plain yogurt would work instead, though the cupcakes may not be as light. Same goes with a lower fat milk.
  5. Why Room Temperature? All refrigerated items should be at room temperature so the batter mixes together easily and evenly. Read here for more information.
  6. Special Tools (affiliate links): KitchenAid Stand MixerCupcake PanCupcake LinersAteco 808 Piping TipPiping Bags
  7. Be sure to check out my 10 tips for baking the BEST cupcakes before you begin!

Keywords: cookie dough, cookies, cupcakes

51 Comments

  1. I’m not sure what I was expecting as I checked for a new recipe today, but it certainly wasn’t this!!! Great surprise though…..these look incredible! Totally trying them soon – knowing that the cupcakes are based off your vanilla cupcakes I already know they’re going to take amazing (because I’ve tried them before and because hellooo! SBA cupcakes!!!) and combined with Kristen’s cookie dough concotions this is a guaranteed success…will get back to you when I try it!

  2. I literally screamed a little when I saw this recipe a few minutes ago. Sally, these cupcakes look PHENOMENAL! I seriously can’t think of many things that are better than cookie dough and cupcakes, and if it’s SBA cupcakes with Kristen’s cookie dough…we have the best dessert ever in our hands. I am totally going to make these as soon as I get the chance! I just stared, mesmerized, at that first picture for about five minutes before I scrolled down. These are my new favourite cupcakes, and I haven’t even tried them yet! 😀 And I hope you and your family had a wonderful Thanksgiving.

  3. Should we allow the heat treated flour to cool completely before we use it or is it better/inconsequential if it is still a little warm? I’ve read that edible cookie dough melds better when the flour is still warm, but those recipes had different ingredients (like with granulated sugar). Thanks for sharing the recipe, it looks really good!

  4. My sister will freak when I make her these! Cookie dough and cupcakes- match made in Heaven! I can’t wait- so excited!

  5. Dear Sally,
    I’m eager for some baking science 🙂 Could you please explain why heat-treated flour is used for this recipe?
    – I live in europe and raw cookie dough as a flavour and as something to eat in considerable portions isn’t that big of a thing over here, so maybe I lack some obvious info? –

    Thanks in advance!

    1. Hi Sina! Raw flour can be a carrier of E. coli unless it goes through a heating process to kill the bacteria. (Think about it– flour is usually baked in a recipe!)

  6. Do you let the cupcakes cool for five minutes then push the ball in? I’m confused by that part of the instructions. One part says to do it immediately and the next says to let them cool for five minuses. I will definitely have to try these!!

  7. These might be my dream cupcake. That frosting looks absolutely divine. I love that her cupcake recipe is based off of yours. Plus the fact that the dough can turn into bake-able cookies shows how thoughtful she was while creating this book. Congrats to Kristen on I’m sure will be a fantastic holiday gift this season.

    1. It’s truly one of the most thoughtful cookbooks I’ve read! So many helpful hints and tricks, plus TONS of delicious recipes 🙂 Hope you love these cupcakes, Courtney!

  8. I got the book on release day and it has been ages since I’ve been this excited for a cookbook. It’s absolutely gorgeous and colorful and full of so many exciting recipes. This might be the first one I make!

  9. For sure trying these. Can the cupcake recipe be doubled or do I have to make it twice? ( I assume the cookie dough parts can be doubled) Only 12 cupcakes is not going to do it for us! Plus I want to take them to a church dinner, so really need like triple the amount.

    1. Hi Julie! For best taste and texture, I always recommend making separate batches of cakes, cupcakes, and such. Cookies are fine to double, but I find you risk over-mixing or under-mixing with cake recipes, which can ruin the taste and texture.

  10. Hi! Does your cookie dough frosting have no brown sugar in it? Just wondering how you got the color of it to look like cookie dough with just powdered sugar! Looks INCREDIBLE!!

    1. I haven’t tried that method and it’s not one of Kristen’s suggestions, so I would start with the milk + cornstarch recommendation.

  11. I got this book on Tuesday and completely forgot I had preordered it. I gave it a quick look but then gave it to my husband to hold and give it to me for Christmas. It will be a slower time and I will have time to savor it 🙂

  12. Okay but how do I make this without spending $11 on flour??
    I love the collab but. I really can’t spend that on flour and this is the BEST cupcake recipe I’ve seen in a long time!! Help!

  13. Question for you Sally? The directions for the cookie dough say to whisk the ingredients together and includes baking soda , but none is listed in the ingredients. Thank you!!

  14. The directions for the cookie dough say add granulated and brown sugars, however, there is no granulated sugar on the list of ingredients. Did I or you miss something 😉

    1. *update*
      I made these and let me tell you they were a hit! Used the microwave to heat treat the flour without any issues. I weighed my flour and had to add a little more for the cookie dough. Definitely need to chill it as the directions state, this makes it less sticky and easier to handle. That cupcake is amazing! So light and airy. I got eighteen cupcakes from this recipe and there was plenty of frosting and cookie dough, actually had some of both left over. Great recipe! Thanks Sally and Kristen 🙂

  15. Hey…just happened to see you on GMA this morning. I had the TV on as background noise and suddenly heard your name. I turned around and almost didn’t recognize you with you new look…very nice! I did recognize your cookies though…sprinkles in the dough make them the best. I have made the cake batter CC cookies many times and they are always a winner.

  16. Hello Sally,
    Can I use like peanut butter cookies, or white chocolate, snicker doole cookies?
    It just a question.
    Thank you so much Sally.
    You have really inspired me to do thing that I though I couldn’t bake.
    Talk to you later

    1. Hi Zoe! You could certainly use another edible cookie dough for this recipe. Do you have the book? She has dozens of different flavors. I’ve tried a few and they’re all so good!

      1. No, I don’t have the book.
        But my mom said we can get it so can’t wait.
        So I’m so EXCITED.
        THNAK YOU SALLY !!!!

  17. Hi Sally
    Love your recipes, thank you! I noticed the cookie dough instruction says granulated and brown sugar but the recipe does not include granulated sugar. Also, the cupcake instruction says baking soda but recipe doesn’t call for soda? Do you mind clarifying that.
    Thanks!
    Blessings,
    Diana

  18. omg!! Yuuuuuumm!! these were amazeballs!!! i didnt have the pasteurized egg whites and i didnt feel like buying them or pasteurizing my own so I followed the cornstarch+milk suggestion amd it workes out prefect. i brought them to work and they were devoured within an hour.

  19. Hi Sally! About how many egg whites is 1/3 cup if I’m gonna pasteurize my own? And since the cupcakes are going to be baked, can I use regular whole eggs instead of 1/3 cup pasteurized? If I used the cornstarch/milk substitution, should it also be used for the cupcakes? Thank you!!

    1. Hi Aly, 1/3 cup is about 3 egg whites. I recommend using only egg whites for the baked cupcakes. You do not have to pasteurize them first.

  20. The best cupcakes I’ve ever made and some of the best I’ve ever eaten! These are amazing. I had yet to make a cupcake recipe that my family liked and my mom said they’re some of the best cupcakes she’s ever had! I used low fat yogurt instead of sour cream and *maple syrup* instead of vanilla because i ran out but they still turned out amazing! The cookie dough was better the first time i made it (lol) with dark not light brown sugar. The vanilla cupcakes are so moist and amazing though! I heat treated the flour in the microwave about 5x (30 sec each) and used what I think was a meat thermometer (I’m doing great here obviously) to measure the temp. So easy! I also used the milk/cornstarch in the cookie dough and 3 actual egg whites (and part of one yolk whoops) in the cupcakes. Even with all my messups they turned out great! I will be making again and again. Thanks so much for all of the terrific recipes- this site basically taught me how to bake and now I use all of your recipes! I can’t wait to try the pumpkin bread and the pecan pie bars for fall!

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