Gluten Free Marble Chocolate Chip Cookies
These gluten free chocolate chip marble cookies are all of your favorites in one! We have classic chocolate chip cookies mixed with double chocolate cookies for a rich and flavorful recipe that everyone will love.

We all know I am obsessed with gluten free chocolate chip cookies. But sometimes I’m craving something a bit more rich and indulgent like my brownie cookies.
In come these gluten free chocolate chip marble cookies! These are all of my favorites wrapped up in one cookie and they are so fun to make! They have crispy edges, gooey centers the perfect amount of sweetness and a rich chocolate flavor balanced with a rich buttery flavor.
They’re made with pantry staple ingredients, the dough requires no chilling and they’re ready to eat in just about 30 minutes!
If you love this recipe, try my chocolate chip snickerdoodles or marble bundt cake next!
Why you’ll love this recipe
- Fun to make
- Pantry staple ingredients
- Dairy free friendly
- Perfectly rich & sweet

How to make marble cookies
In a mixing bowl, combine the softened butter, white sugar and dark brown sugar. Cream with an electric mixer for about 45 seconds or until well combined.
Beat in the egg and vanilla until combined.
Add in the 1 1/4 cup flour, baking soda, baking powder and salt. Mix until combined. Fold in the chocolate chips.
Divide the dough in half- I highly recommend using a kitchen scale to ensure it’s even so we don’t end up with one dough that is drier than the other.

Add half to one bowl and the other half to another bowl. To one bowl, add the extra 1/4 cup of flour and mix to combine.
To the second bowl, add the 1/4 cup of cocoa powder and mix to combine.
Take about 1 tablespoon of each dough and sandwich together. Rip in half, then sandwich together again so you have regular dough, chocolate dough, regular dough, chocolate dough. You can repeat this one more time, but just once is enough. See photos in the post for reference.
Roll into a ball to marble the two doughs together.
Press a few extra chocolate chips on top. Repeat with all dough and add to the prepared baking sheets with enough space in between each.
Bake for 11-13 minutes or until the edges are golden brown. They will continue to set as they cool. Let cool completely, then sprinkle with flaky salt if desired and enjoy!

WANT TO SAVE THIS RECIPE?
How to store and freeze
To store: Once prepared, these cookies will store at room temperature for about 3 days. I suggest storing these in an air tight container at room temperature for best results.
I like to warm them up in the microwave before serving for about 10 seconds so the chocolate melts a bit and they taste good as new!
To freeze before baking: Prepare the cookie dough as instructed, scoop, create the marble layers, roll into balls, then place in a zip lock bag and add to the freezer.
Freeze until you’re ready to bake. Lower the temperature to 325 Fahrenheit and bake for a few minutes longer to account for the frozen dough.
To freeze after baking: Once baked, allow to cool completely, then place in a ziplock bag and freeze for up to 1 month. Reheat at 300 Fahrenheit for about 5-10 minutes or until warm through the center.

Ingredient swaps
Dairy. You can easily make these dairy free by using a dairy free butter in place of the regular butter. Coconut oil is an ok option as well, but butter will yield a richer flavor.
Eggs. Since there is only one egg in these marble cookies, you can safely swap for a vegan option with little to no issue. I suggest either a flax egg or 3 tablespoons of apple sauce.
Sugar. You need a mix of white sugar and brown sugar, which add moisture but also give a crispy edge. I don’t recommend any swaps here, either for other types of granulated sugar or for a liquid sweetener.
Flour. I opted to use the Bob’s Red Mill gluten free 1:1 baking flour, but regular all purpose flour is fine if you aren’t gluten free.

Tips for best results
Weigh the dough. When you divide the dough in half to get one chocolate dough and one vanilla, I highly recommend weighting the dough to ensure one isn’t more dry than the other.
Don’t over bake. Gluten free baking can be finicky, you don’t want to underbake or these marble cookies won’t set, but you also don’t want to over bake because they will get dry. Look for lightly golden edges with slightly soft centers since they will set more as they cool.
Dutch processed vs regular cocoa powder. Either will work here. Natural cocoa powder is acidic while dutch processed is alkaline. Usually, recipes that call for baking soda will need natural since baking soda needs an acid to work.
However, this is slightly more important with things like chocolate cake, and since this recipe also has baking powder which has an acid in it, either will work!

More gluten free cookie recipes!
- Gluten Free Snickerdoodles
- Double Chocolate Chip Cookies
- Gluten Free Sugar Cookies
- Gluten Free Cookie Cake
Lastly, if you want more recipes straight to your inbox, be sure to subscribe to my email list. If you make this recipe, be sure to tag me on instagram and leave a comment below!

Gluten Free Marble Chocolate Chip Cookies
by: claire cary
Ingredients
Base
- ½ cup butter room temperature/softened
- ½ cup white sugar
- ½ cup dark brown sugar
- 1 egg room temperature
- 2 teaspoons vanilla extract
- 1 ¼ cup gluten free all purpose baking flour
- ½ teaspoon baking soda
- ¼ teaspoon baking powder
- ¼ teaspoon salt
- 1 cup semi sweet chocolate chips
For marbling
- ¼ cup gluten free all purpose baking flour
- ¼ cup cocoa powder
Instructions
- Preheat the oven to 350 Fahrenheit.
- Line two baking sheets with parchment paper and set aside.
- In a mixing bowl, combine the softened butter, white sugar and dark brown sugar.
- Cream with an electric mixer for about 45 seconds or until well combined.
- Beat in the egg and vanilla until combined.
- Add in the 1 1/4 cup flour, baking soda, baking powder and salt. Mix until combined.
- Fold in the chocolate chips.
- Divide the dough in half- I highly recommend using a kitchen scale to ensure it’s even so we don’t end up with one dough that is drier than the other.
- Add half to one bowl and the other half to another bowl.
- To one bowl, add the extra 1/4 cup of flour and mix to combine.
- To the second bowl, add the 1/4 cup of cocoa powder and mix to combine.
- Take about 1 tablespoon of each dough and sandwich together. Rip in half, then sandwich together again so you have regular dough, chocolate dough, regular dough, chocolate dough. You can repeat this one more time, but just once is enough. See photos in the post for reference.
- Roll into a ball to marble the two doughs together.
- Press a few extra chocolate chips on top. Repeat with all dough and add to the prepared baking sheets with enough space in between each.
- Bake for 11-13 minutes or until the edges are golden brown. They will continue to set as they cool.
- Let cool completely, then sprinkle with flaky salt if desired and enjoy!
Notes
Comments
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These cookies are absolutely our favorite. I have 2 grandsons with celiac and they loved the cookies. In fact, my husband (who is not gluten free) told me that this cookie is his favorite. I make a lot of GF desserts and they are the best. Thanks for the great recipe!!๐ช
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Amazing! Thank you, Nancy!
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These are delicious! Whole family loves them!
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Love these cookies!!! I love the delicious twist on a classic treat. Looking forward to more gluten-free recipes.
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Didnโt know I was missing these cookies in my life but OMG theyโre amazing! Soft, chewy, just the right amount of chocolate.
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Thanks so much Julia!
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