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100% Whole Wheat Chocolate Chip Cookies Recipe

whole wheat chocolate chip cookies

I don’t understand it, but I’m going to embrace it! I have finally made proper chocolate chip cookies, a feat I have been unable to do since getting married. They’re even healthy with 100% whole wheat flour.

It was like a curse – no matter what troubleshooting I did or how I fidgeted with the recipe on the chocolate chip bag, my mom’s perfect cookie recipe, or the method I used, I always ended up with cookies described this way:

  1. flat
  2. thin
  3. floppy
  4. spread out
  5. crispy on the edges (not in a good way)

I just couldn’t do it.

whole wheat chocolate chip cookies

Then I printed a coupon for whole wheat flour and with it came a recipe. I finally got around to making them, changing the fats to healthy fats, and the results were amazing. Not only is this the perfect melt in your mouth, buttery soft chocolate chip cookie, but it’s 100% whole wheat too. I didn’t even have to use white whole wheat. My hunch? It’s the coconut oil.

Get this recipe, updated and improved with tons of FAQs, in the eBook Smart Sweets, along with 29 other delicious desserts that won’t make you feel guilty! Click HERE for a table of contents.
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100% Whole Wheat Chocolate Chip Cookies

  • Author: Katie Kimball


  • 3/4 c. granulated sugar
  • 3/4 c. packed brown sugar
  • 1/2 c. butter, softened
  • 1/2 c. unrefined coconut oil, melted
  • 1 tsp. vanilla
  • 1 egg
  • 2 c. whole wheat flour
  • 1 tsp. baking soda
  • 1/4 tsp. salt (Use the code kitchenstewardship for 15% off of your first purchase)
  • 1 c. chocolate chips
  • optional: chopped walnuts (use the code STEWARDSHIP for 10% off at that site!) (Mmmm!)

ship kroger


  1. Heat oven to 375°F.
  2. In large bowl, cream sugars, butter and oil for a few minutes with an electric mixer.
  3. Add vanilla and egg, beating until well combined.
  4. Beat in flour, baking soda and salt until well blended.
  5. Stir in chocolate chips and optional nuts.
  6. On ungreased cookie sheets, drop dough by rounded measuring teaspoonfuls about 2 inches apart. The smaller cookies make a better shape and don’t spread out so much.
  7. Bake 8 to 12 minutes or until very light golden brown (centers will be soft). Cool 2 minutes; remove from cookie sheet to cooling rack.


Recipe also works with sprouted flour, but I added an extra 1/4 cup.

If your first batch spreads out too much, add about 1/4 cup more flour. Another alternative that helps sometimes is to give the dough a rest in the fridge overnight to allow the flour to absorb the liquids.

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Ta da! How beautiful are these?whole wheat chocolate chip cookies

Important Recipe Notes:

I made these again some time later, and they turned out totally flat! I had to go back to this post to see if I was lying, or what? It may have to do with having freshly ground flour now, but if your dough seems a little loose, or if your first batch spreads out too much, add about 1/4 cup more flour. Another alternative that helps sometimes is to give the dough a rest in the fridge overnight to allow the flour to absorb the liquids.

whole wheat chocolate chip cookies

I served the first batch at my real food Pampered Chef party, and they went over great. I honestly don’t know if you’d guess that they were “healthy” if you didn’t know.

Find more Healthy Holiday Eats and Sweets at Keeper of the Home today.

whole wheat chocolate chip cookies

I have to give a Healthy Dessert shout out to GNOWFGLINS’ Peppermint Pattie Coconut Bark and Almond Joy Bark, both of which I made today. You should have seen my in-laws eyes pop after I told them there was nothing unhealthy about this candy they were savouring. Seriously good stuff! Find my version of the recipe in Smart Sweets.

Unless otherwise credited, photos are owned by the author or used with a license from Canva or Deposit Photos.

About The Author

41 thoughts on “100% Whole Wheat Chocolate Chip Cookies Recipe”

  1. yum… I”m making these right now, first pan is out of the oven, and they turned out PERFECT, my 4 year old is raving and asking me to call dad and tell him about the cookies waiting… 😉 I did decrease the sugars to 1/2 c. each and I still think its too sweet but I always think that… my son is definitely not complaining!!

  2. I just made these today with my 3 yo daughter and they were a hit. I used expeller-pressed CO instead of virgin, but kept everything the same and had no problems. I usually have the problem with the cookies spreading too much but I kept them small and they cooked PERFECTLY. I made them just over a tbs worth of dough then rolled them into a light ball. I did add quite a bit of walnuts so that might have helped too. Adding to my list :o)

  3. Made these last weekend to take to a lunch – amazing! Love the hint of coconut; perhaps the best chocolate chip walnut cookies I’ve ever had. And you seriously can’t tell they are made with whole wheat at all. I’ll have to try soaking them next time and see how they do. Thanks so much for sharing this recipe 🙂

  4. I decided to try and do a soaked version of these 🙂 I just creamed the butter and coconut oil together and added a couple of heaping tablespoons of yogurt and then mixed in the flour and let it do a full day soak. I added the rest of the ingredients the next day (plus an additional 1/2 c. flour), and they turned out delicious and look beautiful!

  5. We just made these and I think they’re fabulous! Not flat AT ALL. And very moist and gooey – just the way like my cookies. They might just be our new go-to chocolate chip cookie recipe!

  6. Been itching to make these & finally did! Unfortunately I’m still having problems with these – but believe it’s due to the altitude (Colorado). They taste *delicious* – but greasy. I doubled the recipe as I need to take some for snack tonight for the girls’ church activity. After the first pan I added 1/2 c. flour and after the 2nd pan another 1/2 c. If that doesn’t do it, I might try reducing the butter/oil (I’ve noticed some high altitude recipes do reduce the fat).

    1. Julie,
      They are pretty high fat, but yummy. I wish I knew more about high altitude baking, but I’m totally not helpful! 🙂 Katie

      1. Me too! 🙂
        Some things it doesn’t seem to matter & others it does. But I will continue to work with this recipe (I’m thinking 1/3c each of butter & coconut oil), as all who tasted them agreed they are delicious! Thnx!! 🙂

  7. Pingback: What’s in YOUR Lunchbox? A Sweet Ending | Quick and Easy Cheap and Healthy

  8. I commented above about trying to make these, and I just finished the first batch. It’s a chocolate chip cookie miracle! After two years, we finally have beautiful, delicious ww cookies. Thank you so much!

  9. I just left a comment elsewhere about looking for the perfect choc chip cookie recipe – every single one I’ve tried had turned into a pool of crispy butter. I’m trying this one ASAP!

  10. Oh my goodness! I just pulled these out of the oven and I think I’m in love. They are the perfect consistency and the tiny hint of coconut adds so much. Thanks for sharing!!

  11. If butter and coconut oil are too pricey, it would be worth having lard on hand. Good quality, pasture fed type or organic (so you know that the pigs were kept and fed well) Our grandmothers used lard all the time and most pastries taste good with lard in them.

    1. Yes, lard is great, too, just make sure you don’t end up with hydrogenated lard, which the inexpensive stuff usually is. The good stuff is often more pricey than coconut oil. Katie

  12. What would you suggest to do if one doesn’t have coconut oil? I’d love to use it, but I just have a hard time OK’ing the price.

    1. Kim,
      You could always use melted butter for that liquid coconut oil part, but I do think the slight coconut flavor adds something to the cookies. I get it for only slightly more than a pound of butter in bulk, and refined coconut oil (without any flavor) is less than good butter.
      🙂 Katie

  13. Wow! I just made these & they are THE best chocolate chip cookies I’ve ever made! Yum! Thank you so much for posting this recipe!

    1. My son and I were going to make these yesterday but didn’t get around to it…now I’m totally drooling! 😉 Katie

  14. Pingback: Healthy Holiday Treats from Kitchen Stewardship « Catholic Mommy Brain

  15. Wardeh @ GNOWFGLINS

    Katie – Those look like seriously awesome cookies! 🙂

    I’m tickled that you enjoyed the coconut bark recipes! Thanks for linking to them.
    .-= Wardeh @ GNOWFGLINS´s last blog ..Details About the Gallery of Christmas Cookies ~ Next Monday! =-.

    1. Wardeh,
      Girl, you would not believe how many people I have emailed about the coconut bark. Oh. My. Yummy.
      🙂 Katie

  16. Earth Friendly Goodies

    Well now you’ve done it…. now instead of going to bed like I should be doing I have to make a kitchen run to make sure I have the right ingredients to try your recipe. 🙂
    .-= Earth Friendly Goodies´s last blog ..No More Headaches with Natura Zero-VOC Paint =-.

  17. Doylene Brents

    The cookies look great. I will try them. Thanks for sharing. Doylene
    .-= Doylene Brents´s last blog ..The Simple Woman’s Daybook =-.

  18. Pingback: Keeper of the Home : Healthy Holiday Eats and Sweets Carnival

  19. Yay! A healthy cookie recipe! I wonder if you could use Sucanat or Rapadura in place of the sugar?

    1. Stephanie,
      I have been told those sub in for most everything just great, but I haven’t dabbled much in expensive sweeteners.
      🙂 Katie

  20. Amy @ Simply Sugar & Gluten Free

    I am a little nerdy (at best) and find myself wanting to see every recipe you’ve made before so I could see what I thought the problem might be…it’s a curse of mine. 🙂

    Thanks for linking to Slightly Indulgent Tuesdays!

    1. Amy,
      We women love to give advice, don’t we? I’m a “fixer” too. Honestly – grab a package of chocolate chips in a grocery store and read the back. That was my recipe, often with a 1/2 cup of wheat germ or whole wheat flour subbed in for 1/2 cup of white flour. I tried chilling the dough, which often helped, but still not perfect. It was crazy!

      🙂 Katie

      1. I would reduce the sugar to 1/2 cup for each of the white and brown sugars and more than likely they will not spread as much. I have reduced the sugar in my cookie recipes by half with great results. Hope this helps.

  21. I’ve cooked with whole grains for a long time but some of the concepts I’m learning from Nourishing Traditions are new, as is learning to apply them. One question I have is about soaking grains. I notice that you do that for some recipes but not for others, like this one. Are there some guidelines you can give me regarding this?

    1. Leigh,
      I’m pretty new to NT too, only about a year in. Some recipes lend themselves to soaking, but cookies don’t work – there’s no liquid in the recipe in which to soak! To make NT cookies, you’d have to use sprouted flour (either storebought or soaked, sprouted, then dehydrated and ground whole grains). Sometimes I might just skip the soaking or not put it in the recipe, especially if it was posted early on in KS before I was mentioning soaking to my readers, who definitely aren’t all NT practicers.

      I’m also not entirely convinced that soaking grains is 100% necessary. I’m in the midst of a lot of research on that right now, with a post or two to come (hopefully) soon.

      Does that answer your question about soaking? Thanks for the comment, and let me know if there’s anything else I can clear up fo ryou.
      🙂 Katie

      1. Katie, yes, thank you. Actually it relieves me a bit because I haven’t figured out how to do NT “strictly” and don’t want to give up some of our family traditions when it comes to food, especially at Christmas!

        I truly appreciate all the research and writing you do. They are a gift to the rest of us.

      2. Sourdough Sue

        There are several ways to reduce the phytic acid(undesirable) in grains…Soak them,sprout them, use wild yeast (as in sourdough starter in your recipe) or to a lesser degree once your recipe is made, toast it (as in breads) If none of those are possible, just enjoy those cookies anyway! No one’s life is perfection! (But those cookies may improve your less than perfect afternoon!

  22. these look tasty to me (minus the nuts as I’m allergic).
    .-= SnoWhite´s last blog ..Truffles =-.

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