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Gluten Free Cookie Dough Cupcakes

Gluten Free Cookie Dough Cupcakes

Gluten Free Cookie Dough Cupcakes

Today is my gluten free son’s 11th birthday. Happy birthday, Jonathan! He’s still in grammar school (5th grade), and in our town that means that we still have the option of bringing in a birthday treat to serve to the class (yes, even homemade—I know). Whenever anyone else in his class celebrates a birthday, if the teacher hasn’t remembered to tell me it was coming (which is often, thanksfornothing), Jonathan gets stuck with a gluten free granola bar from an “emergency” stash kept in the classroom. *womp womp womp* So when his birthday rolls around, he needs me to bake something so at the very least, we know this will be a granola bar-free classroom birthday for him. This year, that something is these gluten free cookie dough cupcakes. I think they make a statement, and that statement is this: my mom’s gluten free cupcakes are better than the gluteny ones your mom bought. 

Gluten Free Cookie Chips—for Gluten Free Cookie Dough Cupcakes

To make these Statement Cupcakes easier to transport to school, and neater for children to eat in the classroom, I don’t pile on the frosting for the few dozen I’m bringing to school this morning. I just dollop a wee bit of frosting on top of the cooled cupcakes and top them with a chocolate chip cookie chip. It was worth the extra effort to make sure these cookie dough-filled cupcakes don’t just taste special but also look special. Can you tell I’m on a mission?!

Gluten Free Cookie Dough Cupcakes—Step by Step

As I’m sure you’ve figured out by now, these cupcakes have a big ball of edible cookie dough in the center. It actually really pays to make the cookie dough ahead of time, too, since it has to freeze. That’s how it stays soft and mostly unbaked in the oven, even as the moist yellow cupcakes bake perfectly all around. If you’re serving these pretty cupcakes at home, or just not to a bunch of children you’re trying to keep mostly clean, go ahead and frost them for realz. The brown sugar in the frosting means it tastes … like cookie dough. Yup.

Gluten Free Cookie Dough Cupcakes

My kids always say that they hate it when anyone sings the happy birthday song to them. So I had to ask Jonathan: why do you want to celebrate your birthday in school? The answer came back swiftly: To show off your cupcakes, mom. Happy birthday, you little charmer. You don’t look a day over 10 1/2.

Like this recipe?

Prep time: Cook time: Yield: 15 cupcakes


For the cookie dough
1/2 cup plus 1 tablespoon (79 g) basic gum-free gluten free flour blend (52 g superfine white rice flour + 17 g potato starch + 10 g tapioca starch/flour)

1/8 teaspoon xanthan gum

1/8 teaspoon kosher salt

3 tablespoons (36 g) granulated sugar

3 tablespoons (40 g) packed light brown sugar

2 tablespoons (28 g) unsalted butter, at room temperature

1 teaspoon pure vanilla extract

1 to 2 tablespoons milk, at room temperature

1 1/2 ounces miniature semi-sweet chocolate chips

For the cupcakes
1 1/2 cups (210 g) all purpose gluten free flour blend (I used Better Batter)

3/4 teaspoon xanthan gum (omit if your blend already contains it)

2 tablespoons (18 g) cornstarch

1 teaspoon baking powder

1/2 teaspoon baking soda

1/4 teaspoon kosher salt

1 cup (200 g) granulated sugar

8 tablespoons (112 g) unsalted butter, at room temperature

2/3 cup (5 1/3 fluid ounces) milk, at room temperature

2 eggs (120 g, weighed out of shell) at room temperature, beaten

2 teaspoons pure vanilla extract

For the frosting
12 tablespoons (168 g) unsalted butter, at room temperature

3/8 cup (82 g) packed light brown sugar

1/4 teaspoon kosher salt

1 3/4 cup (200 g) confectioners’ sugar

1 tablespoon milk, at room temperature (plus more if necessary)

1/2 teaspoon pure vanilla extract

For decorating
Gluten free chocolate chip cookie chips (optional)

Miniature semi-sweet chocolate chips (optional)


  • First, make the cookie dough. Line a small rimmed baking sheet with wax paper and set it aside. In a large bowl, place the flour blend, xanthan gum, salt and granulated sugar and whisk to combine well. Add the brown sugar, and whisk again, working out any lumps. Create a well in the center of the dry ingredients and add the butter, vanilla and 1 tablespoon of milk, mixing to combine after each addition. Knead the dough together with your hands, adding more milk by the quarter teaspoonful as necessary for the dough to hold together without crumbling. Add the miniature chocolate chips and mix until evenly distributed throughout the dough. Divide the cookie dough into about 18 pieces, each about 1 1/2-teaspoons. Roll each tightly into a ball and place on the prepared baking sheet in a single layer. Place in the freezer until firm (about 10 minutes), and keep frozen until the cupcake batter is ready. The cookie dough can be made weeks ahead of time, frozen and then stored in a sealed freezer-safe zip-top bag.

  • Make the cupcake batter. Grease or line a standard 12-cup muffin tin and set it aside. Preheat your oven to 350°F. In a large bowl, place the flour, xanthan gum, cornstarch, baking powder, baking soda, salt and granulated sugar, and whisk to combine well. Create a well in the center of the dry ingredients and add the butter, milk, eggs and vanilla, mixing to combine after each addition. The batter should be very thickly pourable.

  • Assemble and bake the cupcakes. Fill the wells of the muffin tin about 2/3 of the way full with batter. Place a ball of frozen cookie dough in the center of the batter in each well, and press down firmly to immerse. Top each piece of cookie dough with another teaspoon of cupcake batter. Smooth the top of each cupcake with wet fingers, covering the cookie dough in a smooth layer of batter. Place in the center of the preheated oven and bake until a toothpick inserted in the center of the cupcakes (but not the cookie dough in the center) comes out mostly clean (about 22 minutes). Remove from the oven and allow to cool in the muffin tin for 10 minutes before transferring to a wire rack to cool completely.

  • While the cupcakes are cooling, make the frosting. In the bowl of a stand mixer fitted with the paddle attachment, or a separate bowl with a handheld mixer, beat the butter on medium-high speed until light and fluffy. Add the brown sugar and salt, and beat until well-combined. Add the confectioners’ sugar and mix on low speed until the sugar is absorbed into the butter mixture. Add the milk and vanilla, turn the mixer up to high speed and beat until light and fluffy (about 3 minutes). The frosting should be thick, but not dry. Add more milk by the half-teaspoonful and mix to combine if necessary to bring the frosting to the proper consistency.

  • Frost the cupcakes and decorate. Place the frosting in a large piping bag fitted with a 2-D piping tip (or your favorite tip). Pipe a small mound of frosting on top of each cupcake and sprinkle with a few miniature chocolate chips. Alternatively, place a very small amount of frosting on top of each cupcake (about a teaspoon) and press the underside of a chocolate chip cookie chip onto the frosting to adhere.

  • Concept and frosting from Annies-Eats and allrecipes, as selected by YOU from my Must Make Gluten Free Pinterest Board.



P.S. Did you pre-order up your copy of Gluten Free Classic Snacks? Thank you thank you thank you!

Comments are closed.

  • Jared
    February 7, 2015 at 10:14 PM

    I had a decent length comment and then it seems to have deleted itself when I logged in. :(

    Anyway, first time posting, but I love your blog!
    I’ve always loved to cook, and for about 8 months now I’ve been in a relationship with an amazing guy, who unfortunately has celiac. Your blog has taught me so much, and enabled me to cook him all the foods he can’t usually eat :)
    And they’re good. Every one of your recipes are actually good, not just “good enough” like a lot of gluten free options.

    I’ll be trying this one out soon

  • donna
    February 6, 2015 at 3:16 PM

    could these be made a day ahead? or are they best made the day they are to be enjoyed?

  • youngbaker2002
    February 6, 2015 at 11:58 AM

    happy birthday Jonathan! i promise i won’t sing the happy birthday song.

  • Jennifer S.
    February 5, 2015 at 8:48 PM

    Happy bday big J! These look awesome! Another home run!

  • Katie Ward
    February 5, 2015 at 5:58 PM

    YES!! This will be my 20th birthday treat to myself! Thank you! :)

  • AJAJ2005
    February 5, 2015 at 8:59 AM

    This whole posts makes me smile!! My son is in 5th grade and turned 11 this past New Year’s Eve. He has over 20 food allergies and we have an emergency stash of Enjoy Life bars at his school for the surprise birthday treats we don’t know about a head of time. I can’t wait to make these awesome treats for his Valentine’s Party at school this year! Thanks so much for the recipe and the story reminding me that I’m not alone. :-)

  • Elena, Age 11
    February 4, 2015 at 8:34 PM

    Oops sorry i forgot the picture!

  • Elena, Age 11
    February 4, 2015 at 8:26 PM

    Hi Nicole! off topic of cupcakes but today i made your naan bread. it turned out amazing!!!!! for the bread flour i used the mock better batter(i subbed a scant 1t. of gelatin for the pectin ) i used an equal amount of almond flour in place of whey and reg. tapioca starch in place of the Expandex.(i made the subs becuase i’m df and my mom wouldn’t buy those two ingredients anyway because they are so highly processed) i also used an equal amount of coconut milk in place of yogurt. (also used ghee) these were AMAZING. the dough was amazing the, taste was suberb and the texture basically that of gluten. i could also handle the dough only dredging them in like a T. of flour total for the whole batch. i am making these again SOON!!!!!!!!!!!!!!!!!!!!!!!!!!!!!thankyouthankyouthankyou.

  • Michelle
    February 4, 2015 at 5:06 PM

    Happy Birthday to Jonathan! The kids will be so impressed with those cupcakes! I adore those cookie chips and haven’t made them in a while. Thanks for the reminder!

  • MsGF
    February 4, 2015 at 1:13 PM

    What an awesome Mom you are! Happy Birthday Jonathan!
    These are a keeper! Thanks.

  • Mare Masterson
    February 4, 2015 at 10:42 AM

    Happy birthday to Jonathan! I hope his day is awesome! Oh, Ms. Nicole, I think Amber Masterson is going to love you even more after I make this one! I am going to surprise her this weekend with it.

  • February 4, 2015 at 10:38 AM

    That’s so adorable, what a sweet boy! Happy Birthday!
    I never brought cupcakes to school because my birthday is in the summer. I always wanted to bring them though! I hear now they do half birthdays for the summer kids….

  • Lucy
    February 4, 2015 at 10:27 AM

    Happy Birthday Jonathan! Your mom has the best recipes, enjoy you day :)
    Nicole I love this idea, Thank you for all you do :)

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