Keto Chocolate Chip Cookie Recipe (Healthy, Vegan & Gluten-Free)

Author: Dr. Alexis McNeil

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Time to read: 11 min

chocolate chip cookies cover 2
Finished chocolate chip cookies baked with Detox Desserts ingredient swaps

Keto Chocolate Chip Cookie Recipe (Healthy, Vegan & Gluten-Free)

Prep time

15 min

Bake time

13 min

Servings

18 servings

Category

Cookies

Why you will love this healthy keto chocolate chip cookie recipe

My husband calls this cookie recipe the Detox Desserts “Star Player”. He’s right, it’s the best darn chocolate chip cookie of all time, it’s beloved by all and holds up to any traditional chocolate chip cookie out there. These sweet and salty chocolate chip cookies are chewy, buttery, loaded with rich chocolate, crunchy walnuts and finished with a kiss of vanilla. Take these to any group of non-healthy eaters and no one will have a clue these cookies are designed to improve health.


Whether you’re a seasoned baker or aspiring novice, this chocolate chip cookie recipe will quickly become your favorite. They whip up in a few minutes without any fancy ingredients or kitchen equipment, they store well, travel well and make a perfect ‘anytime’ dessert. This easy, healthy, keto chocolate chip cookie recipe contains far less calories, 3x the fiber, more protein and only 3g net carbs when made with the Grain-Free Flour Swap. One bite will transport you to cookie heaven, without the prerequisite guilt you’d get from a regular chocolate chip cookie.

Recommended products for the best sugar-free, gluten-free and vegan chocolate chip cookies

How the healthy chocolate chip cookies made with Detox Desserts measures up against other recipes

Chocolate Chip Cookie Swap Stats how we measure up

The Detox Desserts* Flour Swap makes it easy to turn these chocolate chip cookies gluten-free, and promotes healthy digestion. The psyllium husk contained in the Flour Swap and inulin contained in the Egg and Sugar Swaps both feed and increase the number of healthy gut bacteria. Plenty of good flora in your intestines can promote a strong immune system along with the added digestive benefits we all love with a healthy dose of fiber. Don’t forget the whole psyllium husk binds waste and toxins in your intestines and helps clear them from the body. This easy recipe for keto chocolate chip cookies is not only free from all the unhealthy ingredients found in traditional desserts but it’s actually gently detoxifying to the body…double win!


The plant soluble fiber from the psyllium husk and the digestive resistant fiber in the inulin work together to slow down digestion of this healthy cookie. The slowed digestion helps provide more blood sugar stability throughout your day which can keep you feeling full and satisfied. This also keeps energy levels constant without the normal sugar crashes one would experience with a traditional, carb-loaded chocolate chip cookie.


I’ve tested this sugar free chocolate chip cookie recipe with Whole-Grain and Grain-Free Flour Swap hundreds of times. They are equally delish and both allow you to make your chocolate chip cookie recipe gluten free and healthy! The Whole-Grain Swap cookies are slightly more cakey in texture, have a few more slowly digesting (healthy) carbs, but I love the hearty, earthy flavor they have. The Grain-Free Flour will provide the lowest carb (keto/paleo) version. The Grain-Free cookies bake amazingly well, with a dense and chewy texture. I LOVE this recipe using both flours in equal parts (⅔ cup Whole-Grain plus ⅔ cup Grain-Free Flour to equal the full 1 ⅓ cup of Flour Swap the recipe calls for). The combination of flours is everyone's taste/texture preference and has become the most popular Detox Desserts* recipe. Plus, mixing the flours is a great way to create a lower carb version of a gluten-free chocolate chip cookie and still allows for a small dose of healthy grains.


For most of my patients, I’m a big advocate for balanced macronutrient meals breakfast, lunch and dinner. Here is an easy way to know what type of Flour Swap to choose to create a balanced macro meal. We’ll use dinner as an example. If your dinner consists of just protein and veggies, I recommend eating a Whole-Grain Swap cookie for dessert to serve as your healthy carb for that meal. Conversely, if you already had a healthy carb with dinner (quinoa, sweet potato, beans, etc.), I would recommend the Grain-Free Swap cookie for dessert so you don’t overeat carbs at that meal. Easy, right?! Balanced macro meals are the best thing you can do to keep your metabolism firing optimally, create blood sugar stability and keep you feeling full and satisfied throughout your day (or night). If you’re a diabetic or need to stay in ketosis, always bake using the Grain-Free Flour Swap.

Featured 1 chocolate chip cookies
Featured 2 chocolate chip cookies
Featured 3 chocolate chip cookies
Featured 4 chocolate chip cookies

How I crafted the perfect keto chocolate chip cookie recipe

Although there are many gluten-free, vegan and keto chocolate chip cookie recipes online, I had trouble finding any that I would actually consider healthy. Fortunately, this keto chocolate chip cookie recipe is easy, can accommodate pretty much every dietary restriction, AND is the most nutritious cookie possible. It’s guilt-free, fuss-free, and you’lI feel good about serving these classic cookies to the people you love. Not even the kids will miss the real thing!


Over the years, I’ve tested the Swap ingredients in numerous 5-star chocolate chip cookie recipes with varying success. DRUMROLL…this recipe came from the back of the Lily’s Chocolate Chip Cookie bag! The flavor and texture of these cookies are hands down, by far, the best. Chewy, buttery, sweet, a little salty, loaded with rich chocolate, crunchy nuts and finished with a kiss of vanilla. This healthy chocolate chip cookie recipe is absolute perfection.


Baked desserts like simple cakes, cookies, sweet breads, scones and muffins are usually straightforward to ‘detox’ and turn out great using the 1:1 swap method, but not all desserts can be made that way. I always recommend using our recipe index as a guide when baking with the ‘Sweet Swaps’ because I’ve tested each recipe at least a few times. This healthy chocolate chip cookie recipe has been tested thousands of times and is requested over and over by my friends and family.

The best ingredients & substitutions for the perfect vegan chocolate chip cookies

Step 1 grain free chocolate chip cookies ingredients
Step 1 whole grain chocolate chip cookies ingredients

Key Ingredients of a traditional Chocolate Chip Cookie: 


  • Flour
  • Butter
  • Eggs
  • Sugar
  • Brown Sugar
  • Chocolate Chips
  • Vanilla Extract
  • Baking Powder
  • Baking Soda
  • Salt

Key Ingredients of a Detox Desserts* Chocolate Chip Cookie:


  • Whole-Grain or Grain-Free Flour Swap: Our gluten-free, high fiber, healthy flour substitutes. (Use Grain-Free for Paleo/Keto version of this dessert)
  • Butter Swap: Our whole food, plant-based butter substitute that bakes and tastes like butter with added health benefits
  • Egg Swap: Our vegan egg substitute that contains 50% more protein than an egg, added prebiotics for digestive support and NO cholesterol.
  • Granular Sugar Swap: Our zero-calorie, zero-carb, naturally sweetened sugar substitute formulated with prebiotics to support healthy digestion.
  • Sugar-free, dairy-free chocolate chips
  • Vanilla Extract
  • Baking Powder
  • Baking Soda
  • Salt

Try Our Gluten-free, Vegan, Paleo AND Keto Baking System

Step-by-step: How to make a healthy chocolate chip cookies

Dry Ingredients:


  • 1 ⅓ cups Flour Swap (I love equal parts Grain-Free & Whole-Grain, but use 100% Grain-Free for keto/paleo version)
  • 1 cup Granular Sugar Swap
  • 1 ¼ teaspoons salt
  • ½ teaspoon baking powder (double for Grain-Free)
  • ¼ teaspoon baking soda (double for Grain-Free)
  • 1 Tablespoon vanilla extract
  • 1-4 Tablespoons hot water (to crumbly consistency)

Wet Ingredients:


Fold-In Ingredients:


  • 1 cup sugar-free, dairy-free chocolate chips (Lily’s brand is a great option)
  • Optional 1 cup chopped walnuts (highly recommend)


1. Preheat the oven to 375 degrees (325 degrees for Grain-Free). Line a cookie sheet with parchment paper.

2. Use a large bowl to mix the dry ingredients well. Add wet ingredients and blend until a thick, smooth cookie dough is achieved and no lumps remain. You can use a stand mixer, hand mixer or a large spoon (my preferred method) to blend wet and dry ingredients. 

Step 2 chocolate chip cookies
Step 2.1 chocolate chip cookies

3. Let the dough rest for about 5 minutes while the fiber absorbs the excess moisture, then stir for 1 more minute. Your dough will become thicker after the resting period. 

Step 3 grain free chocolate chip cookies
Step 3 whole grain chocolate chip cookies

4. Fold in the chocolate chips and walnuts.

Step 4 grain free chocolate chip cookies
Detox Desserts chocolate chip cookie dough when using Grain-Free Flour Swap
Step 4 whole grain chocolate chip cookies
Detox Desserts chocolate chip cookie dough when using Whole-Grain Flour Swap

5. Use your medium cookie scoop to create equal sized dough balls. Roll and press each cookie down on your parchment lined baking tray. Although the cookies will expand as they bake, the fiber doesn’t allow them to spread much. Both Whole-Grain and Grain-Free cookies must be flattened on the cookie sheet.

Step 5 grain free chocolate chip cookies
When using Detox Desserts Grain-Free Flour
Step 5 whole grain chocolate chip cookies
When using Detox Desserts Whole-Grain Flour

6. Bake for about 12-13 minutes or until tops start to crack and bottoms start to turn golden. 

7. Remove from the oven and allow your healthy chocolate chip cookies to cool for a few minutes on the warm baking tray. Then, transfer to a wire rack to cool completely.

Step 7 grain free chocolate chip cookies
Step 7 whole grain chocolate chip cookies

8. Store sealed in the refrigerator for up to 1 week or wrap tightly and freeze for long term storage.


*For best taste, texture and health benefits refrigerate all Detox Desserts overnight before indulging. The overnight chill slows carbohydrate absorption, making these cookies tastier and healthier!

How to store your gluten-free chocolate chip cookies

Store your healthy high-fiber chocolate chip cookies in an airtight container in the refrigerator for up to 7 days. For longer term storage, you can store the cookies wrapped tightly in the freezer.


How to make your vegan chocolate chip cookies stand out

  • Don’t feel locked into chocolate chips and walnuts as your fold-in ingredients. Use any of your favorite sugar-free baking chips and nuts in this recipe. I’ve used this basic cookie recipe to create white chocolate/macadamia nut cookies, milk chocolate/pecan cookies, and cranberry/pecan/white chocolate chip cookies. You get the idea, delicious possibilities are endless!
  • Easily make ice cream sandwiches by stuffing these cookies with our ‘homemade keto ice cream’ recipe. Or stuff these cookies with vanilla or chocolate buttercream frosting for an extra indulgent sweet treat.

Tips for making the best sugar free chocolate chip cookies

  • Make sure your Butter Swap is well stirred and at room temperature before making your cookies, oil separation is normal in the Butter Swap. If you’re having trouble stirring your Butter Swap, pour the entire jar into a high speed blender. Your Butter Swap will stay smooth for a couple months after a minute in the blender!
  • Try using equal parts Whole-Grain and Grain-Free Flour Swap for these cookies. The mixture of flours is my favorite flavor/texture variation in most desserts. If you use both flours, bake at 350 degrees for about 12-13 minutes.
  • Use HOT water in your Egg Swap, the warmth is needed to help the psyllium husk in the Flour Swap open up, relax and absorb the moisture.
  • Let your cookie dough rest for about 5 minutes after you’ve blended the wet and dry ingredients, then stir for one more minute.
  • Roll and press your cookies onto the cookie sheet. Although they will expand as they bake, the fiber contained in the Flour Swap doesn’t allow cookies to spread much as they bake, so they need to be flattened down.
  • I’ve found that giving the cookies a gentle press while still very warm will give the finished cookie a more chewy texture.
  • Make your cookies the day before you plan to serve them. The overnight chill also slows carbohydrate absorption, making your high-fiber cookies tastier and healthier!

Keto Chocolate Chip Cookie Recipe (Healthy, Vegan & Gluten-Free)

Prep Time  Bake Time Total Time
15 minutes 13 minutes 28 minutes

Servings: 18

Calories per serving: 170 cal


Although not guaranteed, we have gone above and beyond to provide you with the most accurate nutritional information for this recipe.




Dry Ingredients


  • 1 ⅓ cups Flour Swap (I love equal parts Grain-Free & Whole-Grain, but use 100% Grain-Free for keto/paleo version)
  • 1 cup Granular Sugar Swap
  • 1 ¼ teaspoons salt
  • ½ teaspoon baking powder (double for Grain-Free)
  • ¼ teaspoon baking soda (double for Grain-Free)

Wet Ingredients



Fold-In Ingredients


  • 1 cup sugar-free, dairy-free chocolate chips (Lily’s brand is a great option)
  • Optional 1 cup chopped walnuts (highly recommend)




Instructions


1. Preheat the oven to 375 degrees (325 degrees for Grain-Free). Line a cookie sheet with parchment paper.


2. Use a large bowl to mix the dry ingredients well. Add wet ingredients and blend until a thick, smooth cookie dough is achieved and no lumps remain. You can use a stand mixer, hand mixer or a large spoon (my preferred method) to blend wet and dry ingredients.


3. Let the dough rest for about 5 minutes while the fiber absorbs the excess moisture, then stir for 1 more minute. Your dough will become thicker after the resting period.


4. Fold in the chocolate chips and walnuts.


5. Use your medium cookie scoop to create equal sized dough balls. Roll and press each cookie down on your parchment lined baking tray. Although the cookies will expand as they bake, the fiber doesn’t allow them to spread much. Both Whole-Grain and Grain-Free cookies must be flattened on the cookie sheet.


6. Bake for about 12-13 minutes or until tops start to crack and bottoms start to turn golden.


7. Remove from the oven and allow your healthy chocolate chip cookies to cool for a few minutes on the warm baking tray. Then, transfer to a wire rack to cool completely.


8. Store sealed in the refrigerator for up to 1 week or wrap tightly and freeze for long term storage.


*For best taste, texture and health benefits refrigerate all Detox Desserts overnight before indulging. The overnight chill slows carbohydrate absorption, making these cookies tastier and healthier!



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Nutritional information

chocolate chip cookie nutritional value

*An important note on carbs:


Net carbohydrates are the sum total of carbohydrates that convert into glucose (therefore raise blood sugar) in the body. Anyone following a keto or diabetic diet should count net carbs NOT total carbs. To determine net carbs, simply subtract the fiber and sugar alcohols from the total carbohydrates on the nutrition label. If you count macronutrients (carbs, fats, protein) you should always count net carbs, not total carbs.


We love your feedback, please make sure to comment and share your experience with this recipe for chocolate chip cookies with the healthy baking community!


Cheers to your delicious health,


-Dr. Alexis

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