Whole Wheat Chocolate Chip Cookies (with sugar!)

35 Reviews / 4.8 Average
This is very out of character for me, but today I am posting a dessert recipe made with sugar! Yes, regular ol’ white (and brown) sugar. But it's okay to treat yourself in moderation, and these Whole-wheat Chocolate Chip Cookies are delicious. Bake a big batch and freeze some for later.
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whole wheat chocolate chip cookie recipe with sugar plated

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We wholeheartedly agree that junk food is okay in moderation, but as I’ve said before I think junk food can be broken down into two very different categories… This recipe for whole wheat chocolate chip cookies will show you how traditional junk food still has a place in the meal plan!

Delicious Whole Wheat Chocolate Chip Cookies

Junkfood the way they used to make it, without all of the additives and artificial ingredients! This recipe for whole wheat chocolate chip cookies is a cut above the processed boxed cookies you’ll find at the store. It uses common but super nutritious ingredients and a little sugar to sweeten things up!

Traditional Junk Food vs. Artificial Factory-Made Junk Food

Now if you are a real food junkie like me, and you get a hankering for something sweet, I would much rather you eat something like these homemade cookies as opposed to a bag of Chips Ahoy. Not only would this homemade version taste a great deal better, but they would also be better for you due to the following reasons:

  1. They are made with mostly whole-wheat flour.
  2. They don’t contain high-fructose corn syrup or artificial additives.
  3. They can be made with organic ingredients.

Whole Food Cookies for Your Real Food Journey

Another reason I am posting this recipe is because some who just recently switched to “real food” may not have a good recipe in their files for homemade cookies and cakes. Before our family’s drastic transformation to real food I used to solely rely on Betty Crocker boxed cake mixes for birthday celebrations. When it came time to celebrate the first birthday after our “100 Days of Real Food” pledge I was at a loss for making a homemade cake from scratch.

So this cookie recipe will be the first of a (very small!) series for those of us that want to occasionally indulge in something extra special without having to rely on mass produced food.

So just to be clear this is one of the few recipes on this blog that would not be “approved” during the “10 Days of Real Food” pledge, but this could also be the perfect reward after working hard to successfully complete your pledge. For a healthier option, make these Paleo Chocolate Chip Cookies!

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Recipe Rating




  1. 5 stars
    I made these, and even did a few substitutions – They turned out GREAT. I used spelt flour and coconut sugar. I served them to “non health food” people, and they had no idea these were a healthier alternative to a traditional chocolate chip cookie.

    Excellent recipe.

  2. I just made these cookies and they have to be one of the best cookies I have ever had! They are full of flavor, soft and almost cake-like. So delicious! I substituted applesauce for the butter and used all whole wheat flour. Great recipe, thanks for sharing!

  3. I made these cookies tonight with fresh ground wheat flour and sucanat/honey crystals. Only thing I added was a little rolled oats (sounded good). Delicious cookies! I can’t wait to make them again. Thanks for a reasonably sized recipe so we can enjoy, but not overdo it.

  4. Something I’ve observed. Some sacks of sugar in the grocery are clearly labeled ‘cane’ sugar, others just sugar. I assume the one labeled sugar means it’s made from sugar beets which almost always are GMO. Something to consider.

  5. I’m not much of a baker, so this may be a silly question, but can you use baking powder instead of baking soda? Does anyone know?

    1. Hi Kristi, baking powder is a leavener just like baking soda, however, it reacts a bit differently than baking soda in the recipe because its actually a combination of a couple of different things. You can certainly use it, but the results may not be entirely the same in terms of how much they rise. Taste wise, I don’t think you’ll find it that much different!

  6. I have made these cookies three times. The first batch was all whole wheat flour because that was all I had. Family loved them. The second batch I used the white flour as listed in the recipe. Everyone complained that they were not as good. Today made my third batch, all whole wheat, and was informed they are great again. Looks like I am going with all whole wheat from now on! Now I do not know what to do with all this white flour!
    Yummy recipe. We did not do cookies that often, but my hubby has a real sweet tooth. These have become his secret guilty pleasure, and a weekly request.

  7. 5 stars
    I am in love with this site. This is the second go-around of doing this type of eating (yep, the crap snuck back in) and I found your blog and decided to follow your recipes for a month. My husband requested chocolate chip cookies last night and I was so pleased I had everything on hand for this one (although it made a dozen cookies). We both loved the cookies.

  8. Do you have any thoughts on how I could alter the chocolate chip cookie recipe using Stevia? I have recently cut all sugar out of my diet due to health issues but allow myself the occasional dark chocolate just so that I can have something, even if it’s something little. I was hoping I could make a batch of these to have on hand when I have a sweet craving because these use to be my favorite, but I wasn’t sure the best way to do it. Thank you!

    1. Assistant to 100 Days (Amy)

      Hi Melissa. Because commercial stevia is highly processed, we do not use it in our recipes. Sorry that I can’t really provide guidance on this. ~Amy

      1. Bummer. I am very new to the idea of stevia, and obviously didn’t know as much about it as I thought. I have tried so hard to cut out processed foods even before having to give up sugar fully. I have noticed a huge difference in my pain since cutting out sugar but have a horrible sweet tooth still and am looking for ways to indulge without causing pain. I had read that honey would have the same affect on my body so I have not even been using that, but it might be worth trying it in a few recipes and seeing how my body responds. Thank you for the information.

      2. Assistant to 100 Days (Amy)

        Hi again Melissa. You know your body, how you feel, and have to make decisions (including what you eat) based on what is best for you. ~Amy

      3. Have you tried coconut palm sugar? I avoid sugar as well and have had good success in substituting with coconut palm sugar, which has a lower glycemic index.

    1. Assistant to 100 Days (Amy)

      Hello Holly. Look for brands at Earthfare, Whole Foods, or the like that contain no soy lechitin. The darker the chocolate the better but aim for >70% cacao. ~Amy

  9. making these right now. looking forward to these. trying to eat a little healthier and been on the look out for a easy and quick choc chip cookie receipe. i usually make the logs lol.

  10. Hi, do you think the Betty Crocker Gluten Free cookie Mix would be ok? The ingredients seem very similar except they use: Rice Flour, semi-sweet chocolate chips (sugar, chocolate liquor, cocoa butter, soy lecithin, vanilla), Brown sugar, sugar, potato starch, potato flour, leavening(baking soda, sodium acid pyrophosphate, monocalcium phosphate, xanthan gum & Salt. Just wondering, they were delicious but not sure what you thought about the last few ingredients. I will try your recipe next time though. thanks and love your site & fb page!

    1. Assistant to 100 Days (Amy)

      Hi Heather. There aren’t any boxed mixes that we recommend because most are full of ingredients that we wouldn’t stock in our own real food pantry. Also, our recipe is not gluten free. Whole wheat has plenty of gluten. If you need a gluten free cookie, there are whole grain gluten free flour alternatives, such as millet, that you could experiment with. Hope that answers your question. ~Amy

  11. These are so good! I did all white whole wheat and they are super tasty. After about 8 minutes, they were a nice golden brown, but a little cakey. I popped them in a little longer in the still warm oven and they crisped up a little. Middle is still gooey and delicious! Thanks for the great recipe!

    1. Assistant to 100 Days (Amy)

      Hi Britney. I am sorry the cookies didn’t turn out the way you hoped. They are a bit more dense than a white flour cookie and but should not have been cakey. I’m not sure what might have happened. Maybe give them another try? ~Amy

  12. 5 stars
    I made these for the first time last weekend and they were awesome! I used coconut sugar in place of both the white and brown sugars and I used the flax + water substitution for the egg and they turned out perfect. Thank you for another great recipe! :)

  13. These are fantastic! I used all whole wheat flour and a almost full bag of mini chocolate chips. The first batch never made it to storage container.

  14. Making these cookies right now with my little kiddo. Can’t wait to take them out of the fridge and bake them. Yum! I love eating healthy and cutting out processed foods, with a cheat once in a while and the fact that we make our “junk food” makes it less processed and happens less often since we have to make it from scratch. We LOVE Lisa and everyone at 100 Days of Real Food.

  15. Hi. I made these cookies today using all whole wheat flour. They were ok for my first attempt. They browned well and were fairly soft. My question is how do I make them a bit more flavorful? They were a little bland, but I don’t want to add extra sugar as I think there is plenty. Is it the whole wheat flour that gives it the more bland flavor/texture rather than white flour? Thanks!

  16. I was curious if you had the nutrition break down! I am going to make these for my nephew who is a Type 1 Diabetic and counts carbs!

  17. Assistant to 100 Days (Amy)

    Hi Becky. You can’t use the coconut palm sugar during the pledge but outside of the pledge, it is something you might experiment with. I use it. It is much less sweet than sugar and my taste buds have welcomed it. I’ve not used the sprouted grains for baking but I think, again, you can experiment. White Whole Wheat flour is a really good replacement for AP flour. It is just a lighter wheat variety but it is 100% whole wheat. Hope that helps. ~Amy

  18. I have a question – if you don’t use the regular white and brown sugar, and instead use coconut palm sugar (and what could you use for brown?) Would it be considered “real”? And would it then be considered “okay” during the 10 day pledge?
    Also – I recently purchased organic sprouted whole grain flour. I have used it in banana bread, and it’s amazing. Would that work for these? I’m still a little unsure of how the flours are all different in the recipes we use them in. (Not how they’re made – I get that, but how the type affects the final product of what you’re making.)
    I used them (with AP flour) for pancakes that turned out great, but I would really like to get rid of the AP flour altogether… not sure if I can though? Thoughts?

  19. I just made these with all wholewheat flour and all brown sugar. I only used 1/4 cup of chocolate chips. But I also added a sprinkle of hemp hearts, some oats, some bran, some young cocoonut flakes and walnuts. They are to die for! :)

  20. Made these last night for my family. I used dark chocolate chips and added 1/4 c oats. Was a big hit with my toddler son. Husband could have used a bit more sweetness but overall great recipe! I especially liked that it made just enough. Will be making again! Thank you!

  21. 5 stars
    Ok, question. First go around, my butter wasn’t right (might have been too cold in the middle still). I used 1/2 www and 1/2 unbleached all purpose. I didn’t refrigerate these as no time. They didn’t brown on top? Second go around everything creamed better, refrigerated and I used all whole wheat. They browned. Any idea why that might occur? I actually prefer the all whole wheat!

    1. Assistant to 100 Days (Amy)

      Hi Alissabeth. You know, baking is such an imperfect art and the slightest variation can make a difference in how a recipe turns out. It could be temperature, texture, consistancy, etc…your guess is as good as mine on this one. ~Amy

  22. My son wants to take cookies for school tomorrow (I will be sending the shaped fruit too!). ;-) Anyway, I can’t even bring myself to make the Toll House recipe (the cc I have on hand) because off all the butter and sugar! Of course when I searched your site, I came up with these! No way a 5 year old will know any better! Thanks for all your great recipes!

    1. Assistant to 100 Days (Amy)

      Hi Lisa. We have substituted coconut palm suger for regular sugar. The only real difference you are likely to notice is color.
      The following comes directly from the Food Babe’s blog (www.foodbabe.org)…”Organic Coconut Palm Sugar…is…completely unrefined and not bleached like typical refined white sugar, helping to preserve all of its teeming vitamins and minerals. It is naturally high in amino acids – has 10,000 times more potassium, 20 times more magnesium and 20 times more iron than conventional sugar. Converting to this type of sugar could also, lower your risk of developing diabetes because it’s glycemic index is half of that compared to sugar.” Goodluck and let us know what you think. -Amy

  23. 5 stars
    These are so delicious! I made them with all white whole wheat flour, used about 1/2 cup of coconut palm sugar instead of the regular sugars, and tossed in 1/2 cup of “Enjoy Life” mini chips. I never would have known that they were whole wheat and refined sugar free if I hadn’t made them myself! Thanks for another amazing recipe!

    1. These aren’t healthy, they are a treat. They are better than store bought or traditional chocolate chip cookies but that doesn’t mean they are “healthy”.

    2. Assistant to 100 Days (Jill)

      Hi Amber. I’m not sure I would say “healthy”, they are still a treat. No matter what, sugar is sugar and should be consumed in moderation. Jill

  24. Your take on Turbinated or Turbinado sugar…

    Just heard of it today for the first time when I mentioned to a friend I was not liking the fact that maple syrup has 200 cal/tbsp. At least the one I purchased does.

    1. Assistant to 100 Days (Jill)

      Hi Eva. The only sugar I really like to use is coconut palm sugar. I think that the Turbinado sugar is still pretty processed, it just has the molasses added back if I am not mistaken. Jill

  25. Why not use sucanat and be eaven better?? It is whole ground sugar cane with all the vitamins the body needs to process the sugar!

    1. Assistant to 100 Days (Jill)

      Hi Kelly. The only sugar substitution I have made is to use coconut palm sugar for the white sugar. And, I use muscovado in place of brown sugar. Jill

  26. Made these cookies for a church snack but used honey instead of sugar and whole wheat flour instead of the white, people couldn’t believe these were healthy and the kids loved them (though they did accuse me of trying the kill them by feeding them something good for them). But my biggest surprise was my husband who thinks all healthy food tastes bland, he took some of them, tried them, and had more before I told him they were a “healthy food”. He actually wants me to make more!