Sign up for my FREE Thanksgiving Email

The Best Gluten Free Chocolate Chip Cookies You’ll Ever Eat

This is the BEST gluten free chocolate chip cookie recipe you’ll ever eat! Made with quinoa flour and coconut oil, these healthy gluten free chocolate chip cookies will surprise you with incredible flavor and chewy texture. Easy to make and best of all, you’d never know they’re gluten free or made without butter!

Prep Time
10 mins
Cook Time
10 mins
Total Time
20 mins

This post may contain affiliate links, which means that I make a small commission off items you purchase at no additional cost to you. Please read my policy page.

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.


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 necessary to get my point across.

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 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.

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, 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 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.
  • 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.
  • 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.

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 SLIGHT 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!

Tips for making gluten free chocolate chip cookies

  1. 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.
  2. 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!
  3. 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.
  4. 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.
  5. Why do you 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.

How to store gluten free chocolate chip cookies

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.

How to freeze gluten free chocolate chip cookie dough

  1. Roll your gluten free cookie dough into balls and place them on a cookie sheet lined with parchment paper. Chill the dough in the freezer for 30 minutes. This is known as a flash freeze.
  2. Once the cookie dough balls firm up, you can transfer them to a reusable freezer-safe bag or container. Cookie dough will keep well for up to 3 months.
  3. When ready to bake, simply bake the gluten free chocolate chip cookies as directed in the recipe. You’ll likely just need to add a few extra minutes of baking time!

Freeze already baked gluten free chocolate chip cookies

If you want to freeze these gluten free chocolate chip cookies after baking, simply wait for them to cool completely, then transfer them to a reusable freezer-safe bag or container lined with wax or parchment paper. I like to place them in a single layer to avoid any cookies breaking. Cookies will keep well for up to 2 months. Once ready to eat, simply thaw out at room temperature and enjoy.

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!

The BEST Gluten Free Chocolate Chip Cookies

4.89 from 34 votes
Course Cookies, Dairy Free, Desserts, Gluten Free
Cuisine American
Keyword gluten free chocolate chip cookie recipe, gluten free chocolate chip cookies, quinoa cookies
Prep Time 10 minutes
Cook Time 10 minutes
Total Time 20 minutes
Serves 20

This is the BEST gluten free chocolate chip cookie recipe you'll ever eat! Made with quinoa flour and coconut oil, these healthy gluten free chocolate chip cookies will surprise you with incredible flavor and texture. Easy to make and best of all, you'd never know they're gluten free or made without butter!


  • 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


  1. 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.

  2. In the large bowl, whisk together quinoa flour, baking soda, and salt; set aside.

  3. 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.

  4. Add in dry ingredients and mix together until combined and a dough forms. Fold in chocolate chips or chocolate chunks.

  5. 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.

  6. 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. 

  7. 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

You can freeze both the cookie dough and the gluten free chocolate chip cookies themselves. Check the full post for freezing instructions!

* Feel free to try using coconut sugar in this recipe. I haven't tried it and the cookies won't likely be the same chewy texture with crispy edges, but they should still work okay. Let me know if you test this method out!

**Feel free to use melted butter or melted vegan butter in place of the coconut oil.

I have only tested this recipe using quinoa flour. I have no suggestions for substitutes.

Servings: 20 cookies
Serving size: 1 cookie
Calories: 201kcal
Fat: 11.6g
Saturated fat: 8.7g
Carbohydrates: 27.7g
Fiber: 2g
Sugar: 15.4g
Protein: 2.2g

If you like these cookies, you might also like:

Paleo Chocolate Chip Cookies

Flourless Peanut Butter Oatmeal Cookies

Flourless Double Chocolate Almond Butter Cookies

Damn Good Paleo Chocolate Chunk Tahini Cookies

Paleo Lemon Poppyseed Cookies

Shop This Post

Download My FREE 7-Day Meal Plan

Download My FREE 7-Day Meal Plan

Join the AK email list and get my brand new, FREE Simple & Nourishing 7-day Meal Plan delivered to your inbox.

    Leave a comment & rating

    Your email address will not be published. Required fields are marked *


    This site uses Akismet to reduce spam. Learn how your comment data is processed.


    Show Comments
    You might also like

    Grain Free Santa Hat Brownie Cookie Cups

    Gluten Free Almond Flour Chocolate Sugar Cookies

    Grain Free Peanut Butter Chocolate Chunk Cookies

    5-Ingredient Vegan Peanut Butter Cookies