Chocolate Chip Cookie Dough Cupcakes

Soft-baked Chocolate Chip Cookie Cups piled high with cookie dough frosting! 

stack of 2 chocolate chip cookie cups

I’m sorry for doing this to you. Really, I am. I took chocolate chip cookie dough and combined it with a chocolate chip cookie dough FROSTING. The frosting is egg free and completely safe and necessary to eat. You just found your new favorite way to eat a chocolate chip cookie, I promise.

You can literally see how soft they are! I love these soft chocolate chip cookies but as cupcakes. And I can’t think of a better frosting for them than the actual cookie dough, can you? I didn’t think so.

3 images of chocolate chip cookie cups topped with cookie dough frosting, cookie dough frosting on a paddle attachment, and chocolate chip cookie cups topped with cookie dough frosting

Baking cookie dough in muffin/cupcake pans is actually easier than making actual chocolate chip cookies. There’s no spreading issues to fear and you’re guaranteed a thick result. Spreading is impossible when the cookie dough has no where to spread inside the cupcake tin. Make the cookie dough like usual and then press 1.5 Tablespoons of it into each tin. Be sure to use cupcake liners to make things extra easy. I love the ridged effect the liners give the cookie cupcakes, too. Oh and bonus: no dough chilling for this recipe!

As the cookie cupcakes cool, make your frosting. It’s safe-to-eat cookie dough in frosting form. The frosting uses the same ingredients in your typical cookie dough: softened butter, brown sugar, vanilla extract, flour, salt, and some milk. There are no eggs or leavening agents presentโ€”both ingredients used for the structure of a baked cookie. Well, you’re not baking the frostingโ€”you’re just eating it. And it is GOOD. Dessert perfection, if I do say so myself. I use mini chocolate chips for the frosting because you get more chips with each bite and it makes the frosting easier to spread onto the cookie cupcake.

2 images of chocolate chip cookie cups in a cupcake pan and chocolate chip cookie cups topped with cookie dough frosting

This cookie dough frosting is egg-free and can be made with heat-treated flour. Raw flour can be a carrier of E. coli unless it goes through a heating process to kill the bacteria. (Think about itโ€”flour is usually baked in a recipe.)

How to Heat Treat Flour

Option 1 โ€“ Microwave

  1. You can heat treat your entire bag of flour or just treat the amount you need in a single recipe. If youโ€™re heating just enough for the recipe, add an extra 1/2 โ€“ 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 anย instant-read thermometerย to test the flour in several places to make sure it has reached 165ยฐF (74ยฐC). If you get a lower reading in one area, stir and heat for an additional 30 seconds until itโ€™s all ready.
  3. Measure the amount of flour you need and use in the recipe, then let it cool completely.

Option 2 โ€“ Oven

  1. Preheat oven to 300ยฐF (149ยฐC). Spread more flour than the recipe calls for on an un-greased rimmed baking pan, such as a 9ร—13 inch baking pan or 9ร—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 165ยฐF (74ยฐC).
  2. If some flour sticks to the bottom or sides of the pan, donโ€™t worry, just leave it there. You used more flour than needed in the recipe anyway. Donโ€™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.

Be sure to try my cheesecake cookie cups, too!

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stack of 2 chocolate chip cookie cups

Chocolate Chip Cookie Dough Cupcakes

4.8 from 12 reviews
  • Author: Sally
  • Prep Time: 15 minutes
  • Cook Time: 13 minutes
  • Total Time: 2 hours
  • Yield: 24 cookie cups
  • Category: Cookies
  • Method: Baking
  • Cuisine: American
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Description

Soft-baked chocolate chip cookie cups piled high with egg-free cookie dough frosting!ย 


Ingredients

Cookie Cups

  • 3/4 cup (12 Tbsp; 170g) unsalted butter, softened to room temperature
  • 3/4 cup (150g) packed light or dark brown sugar
  • 1/4 cup (50g) granulated sugar
  • 1 large egg, at room temperature
  • 2 teaspoon pure vanilla extract
  • 2 cups (250g) all-purpose flour (spooned & leveled)
  • 2 teaspoons cornstarch (cornflour)
  • 1 teaspoon baking soda
  • 1/2 teaspoon salt
  • 1 and 1/4 cup (225g) semi-sweet chocolate chips

Cookie Dough Frosting

  • 3/4 cup (12 Tbsp; 170g) unsalted butter, softened to room temperature
  • 1 cup + 1 Tablespoon (215g) packed light or dark brown sugar
  • 2 teaspoons pure vanilla extract
  • 1 and 1/4 cups (160g) heat-treated all-purpose flour*ย (spooned & leveled)
  • 3/4 teaspoon salt
  • 6 Tablespoons (95ml) milk
  • 1 and 1/2 cups (270g) mini chocolate chips


Instructions

  1. Preheat oven to 350ยฐF (177ยฐC). Line two 12-count muffin pans with liners. Set aside.
  2. Make the cookie cups: In a large bowl using a handheld mixer or stand mixer with paddle attachment, cream the butter and sugars together on medium speed until fluffy and light in color. Mix in egg and vanilla. Scrape down the sides as needed. In a separate bowl, combine flour, cornstarch, baking soda and salt. On low speed, slowly mix into the wet ingredients. Stir in chocolate chips. Dough will be thick.
  3. Press 1.5 Tablespoons of dough into each muffin liner. Bake for 12-13 minutes, removing from the oven when the edges begin to slightly brown and the centers still appear soft. Do not bake longer than 13 minutes. Allow cookie cups to cool completely before frosting.
  4. Make the frosting: With an electric or stand mixer using a paddle attachment, cream together the butter and brown sugar at medium speed. Add the vanilla and beat well. Stir in the flour and salt until doughy. Beat in the milk until fluffy. Gently fold in chocolate chips. Frost cooled cookie cups.
  5. Unfrosted cookie cups stay fresh covered at room temperature for 5 days. Frosted cookie cups must be stored in the refrigerator.

Notes

  1. Heat Treated Flour: Though raw all-purpose flour is fine to use in the cookie cups since you’re baking them, it’s safest to use heat-treated flour in the frosting. See note/instructions above recipe or purchase it online.
  2. Special Tools (affiliate links): 12-count Muffin Pan | Cupcake Liners | Electric Mixer (Handheld or Stand) | Mixing Bowl | Whisk
sally mckenney headshot purple shirt.
About the Author

Sally McKenney

Sally McKenney is a baker, food photographer, and New York Times best-selling author. Her kitchen-tested recipes and step-by-step tutorials have given millions of readers the knowledge and confidence to bake from scratch. Sallyโ€™s work has been featured on TODAY, Good Morning America, Taste of Home, People, and more.

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Reader Comments and Reviews

  1. Kellie Demmler says:
    July 2, 2025

    Will this recipe need adjustments for gluten free flour?

    1. Trina @ Sally's Baking says:
      July 2, 2025

      Hi Kellie, We havenโ€™t tested this recipe with gluten free flours, but some readers have reported success using 1:1 flour substitutes (like Cup4Cup). If you try it, let us know how it goes!

  2. Elaine Verdin says:
    June 6, 2025

    Can these be baked in silicone cupcake pans so I wonโ€™t need the liners?

    1. Michelle @ Sally's Baking says:
      June 7, 2025

      We havenโ€™t tested it but canโ€™t see why not, Elaine. Let us know if you try!

  3. Lynda says:
    May 12, 2025

    I had a hard time removing some of the paper liners.


  4. Emily says:
    May 7, 2025

    Love your recipe! Will these work with brown butter chocolate chip cookies?

    1. Lexi @ Sally's Baking says:
      May 7, 2025

      Hi Emily, yes, you can use browned butter here, just be sure to chill it after browning so that it can be solid (and then softened to room temperature) as called for in the recipe. Enjoy!

  5. lola says:
    April 24, 2025

    This chocolate chip cookie cupcake is my grandsons favorite. I use the mini cupcake tins (makes about 48) with the cupcake liners. after they come out of the oven I invert another tin (bottom down)and press down the freshly baked ones leaving an indentation to put the frosting in.
    yum!!

  6. Donna says:
    March 27, 2025

    Can I fill this with frozen peanut butter?

    1. Beth @ Sally's Baking says:
      March 27, 2025

      Hi Donna, we don’t see why not! Enjoy!

  7. Christy says:
    January 20, 2025

    Can I use mini .muffin pans?

    1. Trina @ Sally's Baking says:
      January 21, 2025

      We’re sure you could, Christy! The bake time will be shorter.

  8. Pam B says:
    November 3, 2024

    How are they without any frosting ?

    1. Lexi @ Sally's Baking says:
      November 4, 2024

      Hi Pam, feel free to leave the frosting off. They’re still delicious!

  9. Lisa says:
    October 9, 2024

    These look amazing! Could you turn any cookie recipe into cookie cups?

    1. Lexi @ Sally's Baking says:
      October 9, 2024

      Hi Lisa, in most cases, any drop-style cookie dough will bake well as a cookie cup. Let us know if you give these a try!