Brownie Cupcakes with Cookie Dough Frosting

Fudgy homemade brownie cupcakes with cookie dough frosting on top. One incredible dessert that you’ll want to make again and again!

brownie cupcakes with cookie dough frosting

There’s also nothing like finishing the day with dense fudgy brownies, cupcakes, and cookie dough.

overview photo of brownie cupcakes with cookie dough frosting

These fudge brownie cupcakes are so chocolatey that your head will spin. They aren’t light and fluffy like regular chocolate cupcakes, nor are they as dense as homemade brownies. But they are so rich, so moist, so fudgy, and will practically melt in your mouth. Eating one is by far, the best chocolate experience I’ve ever had. Yes, the brownie cupcakes themselves are an experience.

Now, let’s move on to the frosting. It’s like the dough from my favorite chocolate chip cookies, but smooth enough to slather onto a cupcake or a graham cracker or a pretzel (try it).

brownie cupcakes with cookie dough frosting

This egg-free cookie dough frosting is 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.

If you enjoy cookie dough inspired treats as much as I do, try these cookie dough cupcakes, cookie dough frosted cookie cups, and cookie dough truffles next. You’ll love them all!

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brownie cupcakes with cookie dough frosting

Fudge Brownie Cupcakes with Cookie Dough Frosting

5 from 10 reviews
  • Author: Sally
  • Prep Time: 15 minutes
  • Cook Time: 22 minutes
  • Total Time: 2 hours
  • Yield: 12 cupcakes
  • Category: Cupcakes
  • Method: Baking
  • Cuisine: American
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Description

Fudgy homemade brownie cupcakes with cookie dough frosting on top. One incredible dessert that you’ll want to make again and again!


Ingredients

Brownie Cupcakes

  • 4 ounces unsweetened or bittersweet chocolate, choppedย (I used Ghirardelli)
  • 1/2 cup (8 Tbsp; 113g) unsalted butter, cut into cubes
  • 1 and 1/4 cups (250g) granulated sugar
  • 1 teaspoon pure vanilla extract
  • 3 large eggs
  • 3/4 cup (94g) all-purpose flour (spooned & leveled)
  • 1/4 teaspoon salt

Cookie Dough Frosting

  • 1/2 cup (8 Tbsp; 113g) unsalted butter, softened to room temperature
  • 3/4 cup (150g) packed light brown sugar
  • 1 teaspoon pure vanilla extract
  • 1 cup + 2 Tablespoons (140g) heat-treated all-purpose flour*ย (spooned & leveled)
  • 1/2 teaspoon salt
  • 1/4 cup (60ml) milk*
  • 1 cup (180g) mini chocolate chips


Instructions

  1. Preheat oven to 325ยฐF (163ยฐC). Line a 12-count muffin pan with cupcake liners or spray with nonstick spray. Set aside.
  2. Make the brownie cupcakes: Melt the chopped chocolate and sliced butter together in the microwave in 30 second increments, stirring after each until completely smooth and combined. Allow to cool for a few minutes. Stir in sugar, then vanilla. Add in eggs, 1 at a time, mixing well after each addition. Mix in the flour and salt.
  3. Pour batter into 12 muffin tins and bake for 20-23 minutes. Mine took 22 minutes. A toothpick inserted in the center will have moist crumbs. Be careful not to overbake the cupcakes.
  4. Make the frosting: While the cupcakes are cooling in the pan, make the frosting. With an electric handheld mixer or stand mixer fitted with a paddle attachment, cream together the butter and sugar at medium speed. Add the vanilla and beat well. Stir in the flour and salt until doughy. Stir in the milk and beat until fluffy. Gently fold in chocolate chips. Frost cooled cupcakes.

Notes

  1. Special Tools (affiliate links): 12-count Muffin Pan | Cupcake Liners | Glass Mixing Bowl | Whisk | Electric Mixer (Handheld or Stand) | Icing Spatula
  2. Heat Treated Flour: Though raw all-purpose flour is fine to use in the brownie cupcakes 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.
  3. Milk: I used vanilla almond milk, but any dairy or nondairy milk would be fine.
  4. Boxed Mix: You could easily use boxed brownie mix as a shortcut, but you would need to adjust the frosting accordingly since the cookie dough frosting recipe below only makes enough for 10-12 cupcakes.
  5. Tip: I find these cupcakes are best served cold. I keep mine in the refrigerator.
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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. John says:
    April 20, 2025

    Hi. Any suggestions for making one and a half times the recipe to adapt this to a 13×9 pan of brownies? Thanks.


      1. John says:
        April 20, 2025

        Thanks! Will do.

  2. Amy says:
    April 2, 2025

    I love these brownie cupcakes! I have always used unsweetened chocolate, but realized I only have Trader Joe’s Poundplus Dark Chocolate with 72% Cacao. Is it ok to use this instead?? Thank YOUUU!

    1. Lexi @ Sally's Baking says:
      April 2, 2025

      Hi Amy, that should work just fine here!