What’s a girl to do when she can’t enjoy a nice spring walk outside because of rain during quarantine? Bake the BEST gluten free chocolate chip cookies on the planet.
Obviously.
Some of you may remember this gluten free chocolate chip cookie recipe from back in 2014 when quinoa was just as trendy as matcha lattes, turmeric, cauliflower and almond flour are now. I’m reposting it now with just a few tweaks. And, even though quinoa flour isn’t as popular as it used to be, these cookies still deserve to be baked because they ARE HONESTLY SOME OF THE BEST COOKIES YOU WILL EVER EAT. I recently tested them again and could NOT STOP EATING THEM. They look, feel and even taste like regular chocolate chip cookies.
FYI: sometimes caps are necessary to get my point across.
These chocolate chip cookies are perfectly crispy on the outside, but ooey-gooey in the middle. They stayed soft for days and they had this SLIGHTLY unique flavor from the quinoa that I absolutely LOVED. I really think that this is one of the best gluten free chocolate chip cookies EVER. But obviously, I’m a little biased. That’s why I need you to make them and report back!
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What flour makes these cookies gluten free?
I first came up with this gluten free chocolate chip cookie recipe by just experimenting also known as the ‘buy a bag of crazy gluten-free flour and see what you can make’ kind of recipe. Luckily for me (and you!) it worked out like magic. TOLLHOUSE I’m coming for you.
My flour of choice? Quinoa flour!
Is quinoa flour healthy?
Quinoa flour is incredibly healthy! It’s naturally gluten free and made by grinding quinoa seeds into a super fine flour (which I do NOT recommend trying at home). Quinoa flour feels kind of like whole wheat flour, and it’s high in both fiber and protein so I love to use it in gluten-free baking.
Not only does quinoa flour provide an amazing texture for these gluten free chocolate chip cookies, but it also makes them a bit healthier with a boost of nutrition, fiber, and protein plus it gives them a slightly nutty, delicious flavor.

Ingredients in gluten free chocolate chip cookies
These chewy gluten free chocolate chip cookies are SO easy to make with all natural simple ingredients. And guess what? They’re dairy free and perfectly thick and chewy without xantham gum — an ingredient often used in gluten free cookie recipes that help to thicken them (no thanks!) Here’s what you’ll need:
- Quinoa flour: I used quinoa flour which is naturally gluten free. It’s also high in protein and similar to bread flour in the fact that it will make your cookies extra chewy and soft. You can usually find quinoa flour at Whole Foods and some specialty grocery stores. I like the Bob’s Red Mill brand best. I recommend toasting your quinoa flour in the oven to remove any ‘bitter’ taste before baking.
- Baking soda: Make sure it’s fresh! I’m serious. If you’re baking soda is more than a few months old, toss it.
- Melted coconut oil: I used virgin coconut oil in this recipe which gives these a subtle coconut flavor, although you can use grapeseed oil, regular butter or melted vegan butter (like Earth Balance or Mykonos) instead.
- Eggs: I like to use a large egg for rich flavor and texture, but I’m fairly certain a flax egg would work well in this recipe if you want to make these vegan-friendly!
- Vanilla: Some people consider vanilla to not be gluten-free as it contains alcohol. My recommendation is to buy alcohol-free vanilla if you’re worried and truly want to make these gluten-free. Or just skip the vanilla and add a splash of fresh coffee. Learn how to make your own vanilla extract here!
- Dark brown sugar: You know I don’t mess around with light brown sugar. Dark brown sugar is truly that much better at creating a flavorful cookie. It has a higher ratio of molasses and so you get a cookie that’s a bit richer, but light brown sugar will work. I haven’t tried these with coconut sugar, but let me know if you do!
- Chocolate: Here’s where you get to be creative. You can use your favorite chocolate bar and chop it into chunks, or just grab a bag of your favorite chocolate chips. If you’re vegan or dairy-free, use dairy free chocolate chips. I love using dark chocolate, but milk chocolate or semi-sweet chocolate chips would all be delicious.
- Sea salt: Don’t you dare forget that sprinkle! Well, I guess you can if you want. I don’t want to be too bossy. But again, these cookies are pretty damn fantastic when they’re a little sweet and salty.

Perfect gluten free chocolate chip cookies in 6 steps
- Toast the quinoa flour. Add your quinoa flour to a large baking sheet and bake it for 9-10 minutes at 350 degrees F before using it in the recipe. This helps to reduce the natural bitterness of the flour.
- Whisk the dry ingredients. In a medium bowl, whisk together all of your dry ingredients.
- Mix the wet ingredients. In a separate large mixing bowl, mix together your wet ingredients until they’re nice and smooth.
- Make the dough. Add the flour mixture to the wet ingredients and mix until the dough forms. Then stir in your chocolate chips. You can use a mixer if you’d like, but I typically just mix the dough by hand.
- Scoop & bake. Use a cookie scoop to grab the dough and roll it into 1-inch balls. Place them on your cookie sheet and bake until they start to turn golden brown.
- Cool & enjoy. Let the cookies cool for a few minutes on the baking sheet, then transfer them to a cooling rack to finish cooling. Top with sea salt and enjoy!

Don’t forget these cookie-baking tips
- Melt then cool your coconut oil. Measure out your coconut oil after it is melted and then allow it to sit at room temp for 5 minutes to allow it to cool off a bit. While your coconut oil is cooling off, you can measure your other ingredients out. This ensures that it doesn’t coagulate with the other ingredients or slightly “cook” the eggs.
- Use dark brown sugar. I love using dark brown sugar because it has a tiny bit more molasses in the flavoring, which makes this gluten free chocolate chip cookie taste just like the real deal. Light brown sugar will also work well in this recipe, they just won’t have as deep of a flavor. And don’t forget to pack your dark brown sugar!
- Make sure your eggs are at room temperature before using. This recipe calls for 2 eggs, and you want to make sure they are at room temp. Simply place eggs in a bowl of warm water for a few minutes before using them in the recipe.
- Test a cookie before you bake the entire batch. I always, always test one cookie before baking. Put it on a cookie sheet then bake as directed. Once it’s done you can see if you need to flatten the dough with the palm of your hand in order to create a thinner cookie, or chill the dough for 10 minutes if the cookies are too flat.
- Why do your gluten free cookies go flat? If this happens I suggest simply chilling the dough for 10-20 minutes before baking. They should bake up perfectly.

Storing & freezing tips
- To store: these healthy gluten free chocolate chip cookies will stay good at room temp in an airtight container for about 4-5 days. If you’re going to keep these cookies longer, I’d suggest freezing the dough or the cookies themselves.
- To freeze: you can either freeze the cookie dough or the fully baked cookies! Get all of my tips and tricks for doing so here.
More cookie recipes you’ll love
- Healthy Oatmeal Chocolate Chip Cookies (vegan & gluten free!)
- Grain Free Snickerdoodles
- Blow Ya Mind Vegan Chocolate Chip Cookies (gluten free, too!)
- Paleo Lemon Poppy Seed Cookies
- Grain Free Birthday Cake Cookies
Get all of my cookie recipes here!
I hope you love these easy, healthy gluten free chocolate chip cookies! If you make this recipe, be sure to leave a comment and rate the recipe below. You can also snap a photo and upload it to Instagram with the hashtag #ambitiouskitchen. Enjoy, xo!
Ambitious Kitchen
Cookbook
125 Ridiculously Good For You, Sometimes Indulgent, and Absolutely Never Boring Recipes for Every Meal of the Day
The BEST Gluten Free Chocolate Chip Cookies

Ingredients
- 2 cups quinoa flour
- 1 teaspoon baking soda
- 1/2 teaspoon salt
- 2/3 cup virgin unrefined coconut oil, melted and cooled**
- 1 1/3 cup packed dark brown sugar (or light brown sugar)*
- 2 large eggs
- 2 teaspoons vanilla
- 1 heaping cup chocolate chips, dairy free if desired
- coarse sea salt, for sprinkling
Instructions
- Preheat oven to 350 degrees F. Add quinoa flour to a large baking pan. Bake quinoa flour for 9-10 minutes. This is known as 'toasting' the quinoa flour and will help get rid of any bitterness. Once done toasting, transfer quinoa flour to a bowl to cool off for 5 minutes. Keep heat in oven.
- In the large bowl, whisk together quinoa flour, baking soda, and salt; set aside.
- In a separate large bowl, mix together melted and cooled coconut oil and brown sugar until smooth. Add in eggs and vanilla and beat again until smooth and creamy.
- Add in dry ingredients and mix together until combined and a dough forms. Fold in chocolate chips or chocolate chunks.
- Roll dough into 1 inch balls and place on cookie sheet leaving 2 inches apart. Bake 8-11 minutes or until edges just being to turn a golden brown. Do not over bake; we don’t want crispy cookies here! If you noticed that your cookies are baking super flat, then you may want to chill your dough for 10-20 minutes.
- Remove from oven and let cool at least 5 minutes on baking sheet. The cookies will need to set and will be a little fragile at first so you have to be a little patient for the edges to harden a bit before removing them.
- Once the edges and bottom harden a bit, transfer to wire rack to finish cooling. Makes 20 cookies, feel free to double the recipe if you want more.
Recipe Notes
Nutrition

These cookies taste fantastic! The quinoa adds such a nice nutty/toasty flavour. Perfectly sweet. Mine ended up quite flat tho, even after chilling the batter. That’s the only reason my rating is not 5 stars…they are flat like pancakes! (Maybe because i made my own quinoa flour?? That’s the only substitution i made)
I’m glad the flavor was delicious! Hmm it could be the homemade flour – let me know if you give it a try with a store-bought flour and if makes a difference.
These cookies are amazing! I’m always looking for better ways to make gluten free dishes. I can say that I’ve never made anything bad from Ambitious Kitchen. Love her cookbook as well.
So glad you love these and the recipes from the cookbook!!
Just made these and they’re really good! I made a mistake and flattened the first batch and they all ran together, but the second batch was done as directed and came out nicely. 😉 I’ll definitely make these again.
I’m glad the second batch turned out well!!
Absolutely delicious! I used olive oil and honey (~1/2 cup) instead of brown sugar and it was much too sweet so I will use less next time. Cookies spread out quite a bit (flat) but I do not mind! Will make again. Thank you for the recipe
Honey is much sweeter than brown sugar, which is where that flavor is coming from! And swapping a granulated sweetener for liquid will make the batter a bit thinner. Glad you enjoyed regardless!
These are the best sugar free, gluten free chocolate chip cookies I have tried. I toasted the quinoa flour first, this helps. I used golden monk fruit instead of sugar and Lily’s chocolate cookies. Very happy with the texture and flavor.
So happy to hear that!
Love, Love, LOVE the cookies I made using your recipe. Thank you for such an easy, precise and yummy cookie recipe. The whole family is in love with them.
Ah yay! I am SO glad you’re loving theses cookies and they turned out great for you and the family!
Follow the recipe exactly and you won’t be disappointed! The toasted quinoa adds a nutty unique flavour. Delicious!
I chilled my dough for 10 mins before baking, and sprinkled Sea salt as directed. Amazingggg
I don’t have any quinoa flour, so I subbed with 1 cup rice flour, 2/3 cup sweet potato flour and 1/3 cup corn flour. It was still pretty liquid then, so I added another .5 cup of rice flour and then it was a really nice texture to roll the cookies out. Much better than many other recipes I have tried, so I will be saving this one. Thanks!
Glad those subs worked well! Thanks for sharing 🙂
These cookies are amazing, they taste just like a reg cookie with added benefits. I love that they have more protein and all the nutrients you find in quinoa. I do have to chill mine a bit but not long i stick it in the freezer for maybe 5 min or less and its perfect for me to roll in my hands.
Thanks so much for the review, Emily! Good to know about the chilling before rolling — great call. Happy you love them!
These were delicious and went down a treat with the whole family. Thank you
I’m so glad to hear that!! Thanks, Rosie!
Had quinoa flour hanging around that I wanted to use up. I was blown away by the soft chewy texture of these cookies! I’ve been baking GF for twenty years and can’t believe I hadn’t really yet discovered how well this flour worked. My wheat-eating friends were equally amazed! The ultimate compliment is having a friend say “I’d never know these were gluten free!”
My first time using quinoa flour and my husband, my toddler, and I all give this recipe two thumbs up! I subbed coconut sugar because it’s all I had available and they turned out great. Leaving them on the cookie sheet for 5 minutes before transferring to a wire rack was critical to keep their shape but worked perfectly.
Woohooo! I’m so happy you all loved these 🙂 And yes letting them chill out for 5 minutes is essential!
I thought the cookies 🍪 were fine.
Thanks for sharing! You might like this recipe more 🙂
When were baking them they got very big but they made enough for 3 people to have.👌 Something was wrong with them. They were also to light.
Hmmm sounds like something went wrong! Did you follow the ingredients/instructions carefully? And did they look similar to the cookies pictured in the blog post?
Thanks for this recipe! I added 1/4 cup gluten free flour to the 2 cups toasted quinoa flour because I like a cake like cookie vs. The gooey kind.
Also used coconut sugar. Cookies turned out nice and brown, I think because of the toasted flour.
So glad that worked out and that you loved them, Maureen! Thanks for sharing 🙂
Amazingly soft and tasty. These are great cookies!! Easy to put together. The batter freezes well, too.
SO happy you’re a fan of these, Jaime! Thanks for the review 🙂
Why do you not recommend grinding your own quinoa flour? I grind most of the gf flours I use myself. It is such a huge savings.
Oh my gosh you saved me with this recipe. I was making almond flour cookies and accidentally added quinoa flour! After lots of cussing, I got myself together and found this recipe and the batch was saved! AND….they are delicious!! Thank you for sharing! I have a new healthier cookie to add to my favorites!! PS I already had 1/2 cup shredded coconut in my dough and it was a nice addition to the texture of this cookie in case you are feeling experimental!