Whole Wheat Chocolate Chip Cookies

These whole wheat chocolate chip cookies have a deeper flavor and a chewier texture than traditional cookies. Walnuts add crunch. The cookies are even better the next day, if you can believe that!

One whole wheat chocolate chip cookie pulled in two

We pinky swear these whole wheat chocolate chip cookies don’t taste healthy. Not even remotely. The whole grain flour in tandem with the walnuts lends the cookies a distinct nuttiness and the chocolate chunks pretty much take things home from there. These cookies, from Manresa Bread in Los Altos and Los Gatos in California, are the first things to sell out. And we SO understand why.–Renee Schettler Rossi

Whole Wheat Chocolate Chip Cookies

  • Quick Glance
  • (5)
  • 30 M
  • 1 H, 35 M
  • Makes about 12
4.6/5 - 5 reviews
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Preheat the oven to 350°F (175°C). Line 2 or 3 baking sheets with parchment paper.

Spread the walnuts in a single layer on a rimmed baking sheet and slide in the oven for 5 minutes. Stir the walnuts and then continue to bake, tossing or stirring every 2 minutes, until they’re golden brown and start to become fragrant, 5 to 10 minutes more. Keep a careful eye on them. Remove from the oven and immediately transfer them to a plate to cool. Coarsely chop the walnuts.

In the bowl of a stand mixer fitted with the paddle attachment on medium speed, beat the butter and brown sugar for about 2 minutes. The mixture should be barely fluffy and almost light brown in color. Be careful not to overmix.

Add the eggs and vanilla, reduce the speed to low, and mix until well combined, about 2 minutes.

In a separate bowl, whisk together the flour, salt, and baking soda. With the mixer still on low speed, slowly add the flour mixture in 2 additions, mixing just until combined.

Switch to a spatula and gently incorporate the chocolate and walnuts into the cookie dough.

For supersize cookies, grab an ice cream scoop or a large spoon and dump the cookie dough onto the prepared baking sheet, leaving plenty of room between the blobs of cookie dough. For modest size cookies, plop a spoonful of dough on the prepared baking sheet. Grab a piece of parchment paper and using your palm or the bottom of a glass, slightly flatten each cookie.

Refrigerate the prepared cookies for at least 1 hour before baking.

Preheat the oven to 325°F degrees (160°C).

Bake the cookies until just barely baked through, 8 to 10 minutes for modest size cookies and 10 to 14 minutes for supersize cookies, rotating the baking sheets after 5 minutes.

Move the baking sheets to wire racks and let the cookies cool slightly. Enjoy immediately or store in an airtight container. The cookies will keep for several days and get even better a day or so later, although eating them warm straight out of the oven is always encouraged. Originally published June 23, 2018.

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    Recipe Testers' Reviews

    These whole wheat chocolate chip cookies are the new gold standard by which I will judge all chocolate chip cookies. What an incredible texture these have! When first baked, they're a bit delicate, gooey, and fragile. By the next day, however, the cookies mature into this moist, chewy cookie that’s out of this world. The structure holds, the brown sugar flavor deepens, and the cookies are buttery and even more delightful. I usually bake my cookies fresh since most cookies are better on day 1 than day 2, but this is the opposite—give me the day-old cookie, please!

    Transferring them from the baking sheet is tricky if they aren’t all the way cooled. I ate one when the chocolate was still liquid and I had to use a fork on a plate. (That’s not a complaint.)

    The bran really keeps the gluten from tightening and must be responsible for the special texture. They will break easily—no snap on these cookies, just a gentle bend will do it. They just kind of bend.

    I put the dough in the refrigerator for about 2 1/2 hours. At 13 to 14 minutes, they were barely done with a bit of structure.

    If I had Googled "chocolate chip cookie recipes," I would most certainly have passed on a Whole Wheat Chocolate Chip Cookies recipe. But I will be adding this to my regular rotation of chocolate chip cookie recipes. I'm not usually a fan of walnuts in cookies, but the nuts and wheat flour worked together to create a nutty, chocolatey, substantial cookie that was perfectly satisfying.

    I baked half of the dough after refrigerating for about an hour and a half and the other half after 24 hours, and while there was a small difference, it was not nearly as pronounced as it can be in other recipes (like the Ultimate Chocolate Chip Cookies).

    However, what truly made a difference was letting the cookies rest overnight after baking. While delicious fresh from the oven, they were definitely best the next day.

    Process-wise, I would probably not pre-scoop the cookie dough onto cookie sheets before refrigerating and would instead just refrigerate all of the dough and scoop while cold to save space in my fridge and just pop the formed dough on sheets into the fridge for a few minutes before baking.

    I have two words for these whole wheat chocolate chip cookies: huge and delicious! These are not dainty by any means, but, man, are they good.

    The whole wheat and the toasted walnuts deliver an earthy, robust cookie. I am never using all-purpose flour in chocolate chip cookies again! I used light brown sugar but would try dark brown next time. I used my 3T cookie scoop and had to use 2 slightly heaping scoops to get to 3 inches wide by 1 inch tall as stated in the header.

    I am tempted to tinker a bit and brown some of the butter and I think all cookies are better with a little fleur de sel sprinkled on top. So worth it! I think they are fantastic warm and they still retain a nice chewiness for a couple days.

    We unanimously sang these cookies’ praises with our mouths full! We loved their superbly moist texture and the heavenly combination of dark chocolate, toasted walnuts, and warm brown sugar. They’re so good you’ll appreciate their generous size—4 inches in diameter—and will want another as soon as you finish one!

    The use of whole wheat flour is wonderful too, marrying better nutrition and pleasure. I baked the supersize cookies on 2 half-sheet baking pans (18 by 13 inches) and 6 cookies fit perfectly on each pan.

    They didn’t touch each other after they spread in the oven. So if your baking pans are similar to mine in size, just divide the dough into 12 portions. The dough is sticky—I recommend using a small piece of parchment when flattening the scoops. The cookies were so delicious.

    Lovely indulgent cookies that achieve richness without being too sweet (unless there is too much chocolate, which some would say is not possible)! Having tasted the real thing, this recipe begged me to make it.

    The recipe is simple and requires a little planning for fridge space but really not too much work. I did watch the walnuts like a hawk and specifically chose a light walnut variety that I know is less likely to have any bitterness, Chandlers.

    The dough comes together nicely and the chunky walnuts and chocolate chunks were nearly the same size. (I chose dark chocolate chunks that were about 1/2 inch square and 1/4 inch thick with 67% cacao.)

    Once they are cool enough to eat, you will find that they’re messy in a delicious lick-the-chocolate-off-your-fingers kind of way, yet not sugar bombs, which I really appreciate.

    The combination of brown sugar and good whole wheat flour really gives a satisfying toothiness to the cookie without screaming “whole grain,” just really yummy. I was tempted to sprinkle some Malden Salt on top but that seemed like gilding the lily a bit. Having recently tried this cookie at the bakery, I was happy to test the recipe and I think this is a nice, rich but not overly sweet cookie—very special.

    I was a bit skeptical at the thought of whole wheat chocolate chip cookies but, after due consideration, I have come to the conclusion that, with the substitution of pecans for walnuts, this recipe is a sure-fire BLUE RIBBON winner!

    These cookies took about 10 minutes to gather and mix. I made the dough the evening before I baked them. Because of the long chill, when I began to scoop the dough, it wasn’t holding together as well as it needed to. I chose to weigh and roll the dough and the warmth from my hands seemed to do the trick. This will take several minutes and quite a bit of the proverbial “elbow grease,” but this recipe can certainly be completely mixed by hand. After all, your great-grandmother baked without power tools and it is understood that our grandmothers and their mothers as well made the best treats EVER!

    Much to my surprise, after letting them cool, the first batch that had initially appeared underbaked turned out to be SPECTACULAR! They were consistent, soft, and chewy, even the following day. So, for a cookie with whole wheat flour and no granulated sugar, this cookie is absolutely delicious. At the end of the day, I could fall asleep knowing that I have done the right thing. Consumed a half dozen much healthier cookies than I otherwise might have.

    These whole wheat chocolate chip cookies are pure indulgence in the comfort of your own home. I love baking and have tried countless recipes and this is hands-down the only recipe that makes me feel as if I were eating something expensive from a bakery but I made it myself!

    The allure of the supersize cookies is their size, especially the 1-inch height. Baking large cookies often results in flat spread out cookies but not these babies. My kids loved the novelty of such a big cookie and needless to say I will be making them again in a few days but I will try pecans next time. The cookies are so soft with a toasted nutty crunch and they stay soft for upwards of 3 days.

    My favorite day for the cookies was day 1 but only because I ate 1 hot out of the oven and nothing can compare to that warm gooey texture. These were still soft on day 3 and are the softest homemade cookie I have ever had.

    These whole wheat chocolate chip cookies are everything chewy chocolate chip cookie lovers dream about (with perhaps the exception of the walnuts, as my chocolate chip purist husband declared these would be much better without them, but I liked the toasted flavor they bring).

    Though you can't possibly imagine they are baked through since they are so huge and bake for such a short amount of time, the texture is spot on—soft and chewy with a lovely crunch from the walnuts. They are, however GINORMOUS, so perhaps take that into account when you bake them.

    This recipe made 14 supersize cookies that would easily have been 30 to 40 more reasonable-size cookies. I used walnut pieces which was nice because I find when I chop walnuts I end up with stray bits of skin and crumbs of skin, which is not nice in a cookie. Baked for 15 minutes—after 10 minutes they were barely colored and very very soft to touch. I let them sit on the baking tray for an hour or so (I forgot about them, to be honest) and they were pretty good in terms of texture then. (I was worried they would be too soft still and even better later that day. Still excellent the next day, too.)

    A note on the serving size—seriously? If you used a smaller scoop and it made more, smaller cookies, I'd give these a 10. But they are a ridiculous size (and I LOVE cookies!) with close to 30g of sugar and 30g of chocolate in each? Too much.

    I was a little suspect of this recipe since it was made with only whole wheat flour, which I often find to be too dense and strong for pastries. At first taste, I did find the taste too strong and dominated by the whole wheat flour. On tasting the cookies a day later, I found them to more mellow and delicious.

    I wonder if the cookies would have been a bit more tender right away with a mix of whole wheat and whole wheat pastry flour. I might also try replacing a third of the whole wheat flour with AP flour.


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    1. 3 stars
      I think this is missing baking powder in the recipe. Calls only for baking soda, but with no acid ingredients to activate the soda, it fails to rise.

      I baked it as written and flavor was great but cookies did not rise at all.

      1. Neel, I’ve double-checked the recipe and the cookbook, and the ingredients are correct. You are correct that it does yield a flatter cookie with fantastic flavor.

    2. Postcript: I still make these cookies on the regular, and I will say that toasted hazelnuts are a GREAT substitution if you want a different nut. My husband gets gleeful when I bake these!

      1. Thanks, Johnisha! Hazelnuts do sound like a fantastic swap and I’d be pretty gleeful too if someone was baking them for me.

    3. I was asked at the last minute to bring cookies to our Christmas Day lunch so I searched the internet for whole wheat cookies as that’s all I had on hand! I’m a moderately experienced baker and I’m always leery of online recipes but I loved this site’s extensive tester reviews and took a chance. I’m so glad I did! I made the dough as described but went for a slice-and-bake method. I formed the dough into a log about 3.5” in diameter, wrapped tightly in plastic and chilled for one hour. Then I made 1/4” slices and placed each cookie on a silicon lined cookie sheet. I baked for 7 minutes, turned the pan, 5 minutes more. As the testers indicated, after cooling they really firmed up nicely! I probably could’ve taken them out earlier but they were on the thicker/denser side because of the log method I chose. Of course, I tasted one and it was delicious! I’m so surprised with whole wheat flour and no white sugar they could be tender just the right amount of sweet.

      A tray of whole wheat chocolate chip cookies

      1. Magnificent, Emily! Love that you made do with what you had on hand and love that you took a chance on us! We test each recipe before it appears on the site—and actually, we test about twice as many recipes as appear on the site because some just aren’t sufficiently spectacular enough to share with others. So we make sure the disappointment stays in our kitchens. Hope you stay a while on our site and let us know when you try another recipe…

    4. Loved it! My boyfriend said these were the best cookies he’d ever had. I pretty much stuck to the recipe with the few minor changes:

      Walnuts were already chopped, so I spent less time toasting them
      Cookie dough spent 3 hours in the fridge
      Each cookie was a little bigger than 1 Aussie tablespoon = 20 ml
      I have a convection oven, so I adjusted the temperature to 165°C and they baked for 8 minutes

      These were delicious! And you’re right, they tasted better the next day. The smaller cookie size made for a larger # of cookies, so we froze the rest we didn’t eat :D

      1. Mela, thank you so much for sharing your experience with this recipe! Love to hear this! So glad you are as enthralled with these cookies as we are. Appreciate you taking the time to try them and to let us know how it went down. Looking forward to hearing which recipe on the site you try next…!

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