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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:
- They are made with mostly whole-wheat flour.
- They don’t contain high-fructose corn syrup or artificial additives.
- 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!






Jennifer says
I love this recipe! As is, makes a delish cookie. I have made it with 1/2 butter 1/2 coconut oil when I was low on butter and they turned out great as well. For a vegan version I have made 1/2 coconut 1/2 applesauce to sub for butter and it turns out a delish pillow cookie. Thanks for a great recipe! Would love an oatmeal chocolate chip recipe one day.... :)
Danielle says
Are these cookies good to make ahead for a trip or maybe freeze?
Assistant to 100 Days (Amy) says
Yep, should work fine! :)
Renu says
What do you think about chocolate chips that are using Stevia (they sell them at Whole Foods). Helps cut down the sugar?
Assistant to 100 Days (Amy) says
Hi Renu. Lisa doesn't really use stevia. She buys the Enjoy Life brand of chocolate chips also available at Whole Foods. ~Amy
Paige says
Oh my goodness these are so yummy! I just made them with
my 3 year old and they are a big hit. I did the wheat white combo
but next time I will try all wheat.
HeatherH says
I made these for the very first time the other day, and they came out great! They were fluffy and moist, not all thin like the ones you would buy from the store. They had a great taste to them, and I will be making these from now on! I ended up using mostly the King Arthur white- whole wheat flour. I will say that my husband didn't like them as much as I do, but he will eat them and that is all that matters! Thank you for sharing this awesome recipe!
Kara says
These are Wonderful!!!! I made them with 100% whole wheat flour. Instead of refrigerating the whole batch, I just popped the pan in the freezer for 5 mins. before baking. I also baked them on the top rack, so the bottoms wouldn't over bake, for about 9 mins. The were just as good as regular.....maybe even better.....yummy :-)
Melissa Shirts says
my kids and I make these all the time. We love them! Thanks so much for the recipe and keep inspiring everyone! :)
Rainer says
What is the purpose of using two different types of sugar?
Lisa says
Mainly for flavor!
Allison says
These cookies are AWESOME!!! Ive made three batches of them and no one can tell that they are a healthier version! LOVE this recipe Thank you!!
Allison says
of course 5 stars!
T. Kelly says
Made these last night and they were PERFECT!!! I usually cut a recipe in half because I DON'T want there to be a lot extra (I have zero self control when sweets are available!) and this was just the right amount for our family of 5...with a little extra.
Buffy McLaughlin says
I just made two batches of these, one with red fife flour and one with spelt. I used the little bit of white flour recipe called for and kept dough chilled. They both were delicious husband and kids all loved them!
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Abbey says
Do you have a good oatmeal raisin cookie recipe??
Assistant to 100 Days (Amy) says
Hi Abbey. Nope, not at this time. I searched a bit and could not find one to forward to you the followed "the rules". ~Amy
Amy H. says
Abbey, I modified Lisa's Pecan Maple Breakfast Cookies (in the recipe index) to be more of an oatmeal cookie and they are wonderful! I swapped the amounts of whole wheat flour and oats (so that there were more oats than flour), and then I substituted honey for the maple syrup. You could do the same and also swap raisins for the pecans and you'd have a terrific oatmeal raisin cookie, in my opinion. You could add another Tblsp. of maple syrup or honey if you wanted them to be more of a treat than a breakfast bar.
Franki says
Yum! I used white whole wheat and oats instead of the AP flour. I also used 1/2 cup of coconut palm sugar instead of regular white. I find that the white stuff makes one of my kids go insane behavior wise:) I also needed to make these dairy free so I subbed Earth Balance coconut spread instead of butter. I added enjoy life mega chocolate chunks and Eden brand juice sweetened dried cherries. Great recipe and easily adaptable. I refrigerated them as suggested and they puffed up nicely. They came out a bit softer than usual cookies probably because there was no AP flour I'm guessing.
Christy says
What brand of chocolate chips do you use? Thanks
Assistant to 100 Days (Amy) says
Hi Christy. Lisa often buys these: http://www.enjoylifefoods.com/chocolate-for-baking/mini-chips/. ~Amy
Kari says
I just made these and since I only had 1/4 cup of butter on hand, I used half butter and half coconut oil. I also added in a tablespoon of (freshly) ground flax. I made small cookies, perfect size for my two toddlers, and ended up with 24 cookies =). While I must admit I prefer a "traditional" chocolate chip cookie, these were pretty delish! Definitely satisfied my sweet tooth tonight.
Kali H says
I LOVE these and the amount the recipe makes is perfect! The taste of whole wheat flour does take some time to adjust too but we're getting used to it at my house. I want to experiment with different chips soon. I've been sharing this recipe with my family and friends and they love them too.
Raquel says
Just made these, All I had was organic unbleached flour, so they were not as healthy as having whole wheat, but turned out wonderful.
Courtenay says
Just made these cookies for the first time and they are great! After reading some of the comments I added a half cup of whole oats and everyone likes them. Thank you for another great recipe; this will definitely be my go to chocolate chip recipe. ps-I used my small cookie scoop and was able to make about 24 cookies!
Erin says
Hi, I was wondering if it would work to premix the dry ingredients so they are ready in the pantry for a special treat? Thanks!
Assistant to 100 Days (Amy) says
Hi Erin. Whole wheat flour should be kept in the fridge or freezer in order to keep it from going rancid. ~Amy
Rachel says
I bake quite frequently and I find the best way to freeze the dough is to portion it out on a cookie sheet and flash freeze it just until it's no longer sticky. Then you can place them in a freezer bag to freeze completely and hang out until you need them. I've done it with traditional chocolate chip cookie recipes and white whole wheat cookie recipes with great success, although I haven't had a chance to try it with this recipe just yet! I bake them straight from the freezer and just watch them during the last few minutes in the oven, adding a couple extra minutes as needed.
Kathy says
Hey, I make my chocolate chip cookies using organic oat flour all of the time with wheat pastry flour, but please don't tell my kids. I sometimes put in oat bran as well. I have used part coconut oil instead of all butter and they turn out just fine. I haven't used coconut sugar, where can I find it?
I have never had much luck saving dough and baking it later, any tricks you can share?
Assistant to 100 Days (Amy) says
Hi Kathy. You can find coconut palm sugar at places like whole foods or other healthier food stores. Traditional grocers might carry it as well (mine does) or you can request that they do. Regarding freezing, I've had much better luck freezing the cookies than freezing cookie dough. :) ~Amy
Jamie Dunson says
These just do it when that sweet tooth comes.
Assistant to 100 Days (Amy) says
Wow, Jammie. You are on a comment role! :) Glad that you are enjoying the blog! ~Amy
Jamie Dunson says
And to think I'm only half way through those recipes, lol. This blog has really changed my life, I love what you all are doing. I'm so blessed to have found it when I did. Thank you, thank you!!!
Franki says
A big hit! We recently found out that my daughter may have a nut allergy so I wanted to make a dessert to bring to a family party we have tomorrow. Though I've been moving towards organic and whole grain food for years I've definitely been a consumer of "organic junk food". I'm new to cooking and baking most things from scratch and cutting out the processed foods. Therefore I didn't feel like using all purpose flour and sugar quite yet. I used the brown sugar but subbed maple syrup for the white sugar (1/2 :1 ratio). I also used all whole wheat pastry flour. I doubled the recipe but only used about 1 cup of chocolate chips for the two batches. We combined enjoy life brand and grain sweetened chocolate chips. This gave the cookies a really rich flavor. Because of my substitutions and the fact that I didn't take my butter out of the fridge early enough the batter was pretty sticky to deal with refrigerating it before spooning it out really helped! Thanks as always for sharing such wonderful recipes!
Jill Oliver says
In a lot of your recipes you say whole wheat flour. I live in England and we have wholemeal (which apparently is the same as your whole wheat) plain flour and wholemeal selfraising flour. If your recipe needed self raising flour would you state that.
Thanks
Assistant to 100 Days (Amy) says
Hi Jill. Lisa doesn't use self rising flour. :) ~Amy
Tanya says
Can these be made by hand? We don't have an electric mixer. Thank you!
Assistant to 100 Days (Amy) says
Hi Tanya. Sure, you can. It just requires a little more work. ~Amy
emily says
can you use coconut flour instead?
Assistant to 100 Days (Amy) says
Hi Emily. Coconut flour absorbs a lot of liquid and I believe it would require changing the recipe a good bit. I can't advise you, however, as my experience baking with it is somewhat limited. ~Amy
Amanda says
Have u ever tried to sub the reg sugar for coconut sugar? Ps thanks for all u do!!
Assistant to 100 Days (Amy) says
Hi Amanda. We've not tried in this recipe so we can't predict the outcome. I do use coconut sugar often in my baking and almost always successfully. ~Amy
Mandy Luna says
You could use spelt flour, coconut oil and coconut palm sugar instead and they would be just as good!
Jodi says
Sounds like a good recipe. How long & what temperature to make it in pan?
Thank you!!
Assistant to 100 Days (Amy) says
Hi Jodi. The recipe specifies 375* for 7-9 minutes. ~Amy
Danielle says
Too funny, was thinking about making this recipe in a cookie bar form vs cookie cake, so glad to know it is doable!! One question I have on Whole-wheat flour, is whether there is a 1:1 ratio for subbing out white flour, and does anything else need to be included??
Thanks for all you do!
Danielle
Assistant to 100 Days (Amy) says
Hi Danielle. You do not need to change the amount. It would remain a half cup. No other changes are necessary. ~Amy
Jennie says
I'm confused. How much partially hydrogenated soybean oil do I use? And do I add the caramel coloring at the end?
Just kidding. I love that I can read over your recipes and all of the ingredients are normal, regular items. Thanks for sharing this!
Assistant to 100 Days (Amy) says
That made me chuckle. :)
Zoe says
I bake cookies quite regularly with my kids using this as a base recipe. I use coconut sugar instead of white/brown sugars, and all whole wheat flour. I also throw in flax, bran, and oats or whatever I have in my pantry. Then I add unsweetened organic coconut and pecans or walnuts, sometimes even dried cranberries or raisins. The added dry ingredients create a chunkier, bulkier cookie which we enjoy. It doesn't seem to matter how many ingredients I add, they always get gobbled up happily by family and friends (often with a recipe request)! This last batch, I didn't have chocolate chips so I chopped up an organic dark chocolate coconut bar. Amazing!
Vicki Lea says
Kristen....I believe the Enjoy Life brand are vegan. I would also love to know what combination of GF flour would work in this recipe, I am GF as well. Oat flour and brown rice...maybe?
Assistant to 100 Days (Amy) says
Hi Vicki. If you experiment with a gluten free version, let us know. Here is an alternative recipe from Deliciously Organic: http://deliciouslyorganic.net/grain-free-chocolate-chip-cookies-paleo-primal/. ~Amy
Jennifer says
Can you substitute the brown and white sugars for coconut sugar?
Assistant to 100 Days (Amy) says
Hi Jennifer. We've not tried. Let us know if you do and what you think. ~Amy
Jenny says
I just made these tonight, subbing 1/2c coconut sugar for the 1/2c combined sugars called for, and they came out great! I added walnuts to the about 1/3 of the batch, and everyone at my house is happy. :)
Kristen says
What chocolate chips do you use? Do you know a good vegan brand?
Vicki Lea says
I believe Enjoy Life brand are vegan....
Sue says
For those readers who are gluten free, I wonder if Rice flour or another alternative would work as well?
Assistant to 100 Days (Amy) says
Hi Sue. We have not adapted this recipe to be gluten free. You are welcome to experiment and let us know your results. ~Amy
Sandy says
I have not tried myself yet but I have read that if you use whole wheat pastry flour your baking will not be as dense as when using regular whole wheat. Has to do with how it is ground I believe.
Gayle says
It's actually not about how the flour is ground. Pastry flour is made from a blend of soft wheat and hard wheat. Using it makes a more tender dough than using all purpose flour because pastry flour is lower in gluten. In baking school we used it for pie crusts - more tender than using bread flour or AP flour, a little stronger than cake flour.
Liz says
Can I substitute spelt flour for wholewheat flour?
Thanks! LOVE this site.
Assistant to 100 Days (Amy) says
Hi Liz. We've not tried spelt in this recipe but I think it will work. Let us know. :) ~Amy
Ema says
I use spelt flour for these cookies all the time (and don't use any white flour at all as the recipe suggests) and the cookies turn out great, super delicious and moist, my husband and kids love them! (and I do too, of course!) :)
Liliya says
I didn't see it mentioned anywhere, but can you freeze these cookies? Or maybe just freeze the dough? I don't eat a lot of cookies, but when my daughter goes to her grandmother's house, she gets to eat the worst cheapest processed treats possible, so I thought I would make them myself and take them there, at least if she eats sweets they won't be full of chemicals. But I don't want to keep cookies in my house all the time, that's why I just wanted to freeze the leftovers, so I can get them out only when I have to. Thank you
Assistant to 100 Days (Amy) says
Hi Liliya. You can freeze them as cookies or dough. :) ~Amy