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

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!

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325 thoughts on “Whole Wheat Chocolate Chip Cookies (with sugar!)”

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Recipe Rating




  1. Any special reason a mixer is needed? The recipe doesn’t seem that different from regular chocolate chip recipes which are easy to do with a spoon

  2. I made these two days ago with all whole wheat flour, did not use white flour and I was very curious how it would taste and all of my kids loved them! We are slowly transitioning to whole wheat flour to a healthier living. I will be making these often! Thank you Lisa for anther great recipe that didn’t dissapoint ☺️

  3. 5 stars
    Hi!
    Can this batter be frozen for future use, or is it just as good to make a few extra cookies and freeze those?
    Thanks!
    p.s. I love this recipe and it has been well-received by everyone I treat! :D

  4. Hmmm, mine seriously flattened out, and even dripped off the cookie sheet! I used all whole wheat flour, but other than that, followed the recipe exactly. Where do you think I went wrong?

  5. Lauren Russell

    I consider myself to be a good cook and terrible baker. These turn out perfect every time. I think the tips on temperature really help. No more sad flat cookies for me, and they taste great! Thanks.

  6. Could I sub earth balance vegan “butter” whipped organic spread for this? My son is allergic to dairy.
    Thanks!

    1. ive also used butter flavored crisco and works fine. just remember to always weigh out 20% less of the amount of butter called for and replace it with water to get the same effect

  7. Love this recipe and feel a little better about serving these cookies to my family. I don’t even use the white flour in this recipe . I use all wheat 1/2 and 1/2 flour and my loves it. Great recipe!

  8. 5 stars
    The whole family ate ’em up, and asked for more !!!! I used mini chocolate chips. It turned out wonderful !!!

  9. 5 stars
    We use whole wheat flour instead of white and the pastry flour. We love them!!! I pre-make these and freeze them to have ready to pull out when company comes over. I have also used coconut sugar when we were out of of cane sugar and they were just as fantastic.
    Thank you for sharing!

  10. I love your recipes. They are all healthy. You really know what is healthy and what is not. I’ve started trying some of your recipes.

  11. 3 stars
    My cookies came out dry. When I was mixing the ingredients I couldn’t even get all the flour incorporated and had to add mor butter. The cookie dough seemed stiff and hard but I cooked it up anyways and they are pretty dry. The only things I did differently were to use whole wheat and white wheat flour, and madava’s better baking blend of cane sugar and coconut sugar.

    1. Try measuring the flour by weight rather than volume. I do this for all my baked goods including bread. Whole wheat flour is heavy and this
      just might fix that. I used all fresh ground whole wheat and it was great.

    2. Two things come to mind. Sugar is hygroscopic. I don’t know if coconut sugar is. Also, sometimes your flour will be dryer than at other times and may obsorb more liquid. If cookie dough is too dry, add milk a tsp at a time until the dough seems right. Freshly ground whole wheat absorbs less liquid than flour which has been stored a while.

  12. I should also mention that she can’t have molasses, that is the reason for no brown sugar. Thank you once again.

  13. Have you tried these with honey? I have a sister who can’t brown sugar or anything with brown sugar in it. I have been using our new life of “Real Food” to help her find some things she is able to eat.

    1. Amy Taylor (comment moderator)

      Hi Lou Ann. Nope, sorry. Lisa has only used sugar in this one. Curious if she can have palm sugar?

  14. I made these for a play date at our house with 2 other families that are health conscience like we are. They were a huge hit! Definitely making these again for our next get together.

  15. 5 stars
    Awesome! I general I am not a fan of whole wheat flour (though I am trying and getting better over time), but these are Amazing! I prefer these whole wheat cookies to regular white flour ones (so does my 3 year old). We have now made these several times (with all whole wheat flour) and will never use another recipe! Thanks so much!!

  16. I just made these cookies with all whole wheat and subbed coconut palm sugar for the sugar….if the cookies are anything like the batter, WIN!!!

  17. 5 stars
    Delicious!!! I made them with all whole wheat flour and they are out of this world! I’ll never make white flour choc chip cookies again!

  18. Just made these and LOVE them!! Seriously, don’t miss the ton of sugar that is usually in cookies. Cannot wait for my kids and husband to try them!

  19. My hubby was craving cookies and wanted to stop at a bakery. I told him I would make him cookies at home knowing I had this gem of a recipe ready and waiting. He loved them and my 9 year said they were the best cookies he has ever had! Thank you!!!

    1. I’ve made cookies with both and with no noticeable difference. Baking purists will say to use unsalted, which i usually do now, but both work equally well.

  20. I am new to baking-after creaming the butter, sugar, eggs, and vanilla for a while, my mixture still had small chunks of butter in it. What am I doing wrong? Does that mean that the butter I am using is too cold? Or is that the texture that the mixture is supposed to be?

      1. I used frozen butter so I softened it in the microwave first. Could this have been the problem? The butter may not have been soft enough?

      2. Room temp my dear. I touch it with my finger, when it squishes it’s ready. Haha. Just use a fork to mash up the pieces of butter if it happens again.

  21. Do you recommend coconut sugar as a replacement? I’ve baked with it before and it was wonderful, but I am new to the real food cooking and wonder if it falls under the “ok” list?

    1. Assistant to 100 Days (Amy)

      Hi Melissa. Lisa doesn’t really use coconut sugar but it is a good alternative to the refined stuff. I use it in my morning coffee. There is some question as to its sustainability, so look for one that is sustainably sourced. ~Amy

  22. I read through 10 of the 18 pages of comments before I gave up and just asked my question. So I apologize if it has already been asked! Have you tried to form the dough into balls and then put it in the freezer? I ask because my son’s school had sold pre-formed frozen cookie dough and, before starting to eat more real food, this was a great, quick snack. It would also keep me from eating all the cookies at once! :)

  23. Florence Mascarenhas

    What is a stick of butter in your choc-chip cookie recipe. You say it is equal to 8 tablespoons. Could you please tell me how many grams is a stick of butter.

  24. I am not a baker in any sense. I have messed up cakes that come in a box. But these turned out GREAT!! Gave them to my toddler who has never tasted chocolate chip cookies before and he loved them. I’ll be making these again. Love knowing what’s going into the food I’m making for my son. Thanks again!