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Whole Wheat Chocolate Chip Cookies

These are the softest whole wheat chocolate chip cookies you’ll taste. Described as “more chocolate than cookie”, you’ll be amazed at how delicious whole wheat can be.

whole wheat chocolate chip cookies on a plate |

I can feel you rolling your eyes. I can sense it from here. This world does not need another chocolate chip cookie recipe for goodness sake. You can’t look anywhere online without seeing someone touting that their chocolate chip cookie recipe is the best. Well friends, today I join those annoying ranks. These really are the best whole wheat chocolate chip cookies around. And because they’re whole wheat, you can tell people you’re pretty much making health food!

When I was five I asked my parents for a cookbook. I got an ABC cookbook for my birthday and for years used the “C is for chocolate chip cookie” recipe quite happily. Then one day, my friend Anne made cookies and the skies opened, angels sang, and birds flew in the window and helped me clean my house. The cookies were that magical.

She gave me the recipe and for over a year I just couldn’t get it right.  I tried different kinds of flour, bought a new box of baking soda, but nothing made them taste the same as when Anne made them.  I finally realized this recipe MUST be mixed by hand with a simple spoon or fork.  If you put it in the KitchenAid or other mixers, you will ruin it.

Today, I serve these cookies every afternoon for Jack and my nephew when they get home from school. You may think I’m trying to seem like a total boss at being a mom – cookies in the afternoon while they do homework, a roast in the oven.


I make these cookies because they are the one thing I can hold over their heads when they are being complete aholes in the morning or on the drive home from school. Nothing makes those punks shape up like saying “I guess you don’t want cookies today…”. They’re so predictable.

Because these cookies are whole wheat, you can feel good better about giving someone a sweet snack. Unlike their white flour brethren, whole wheat cookies have some girth to them and allow you to feel full on fewer cookies. When baking with whole wheat flours, you’ll want to add one tablespoon of vital wheat gluten per cup of flour. The vital wheat gluten gives the cookies the bounce and fluff you’d find in normal flours. You can read more about grinding your own wheat, whole wheat flours, and my love of whole wheat baking in this post.

whole wheat chocolate chip cookies on a tray |

I make a batch of these cookies every week. I pre-make the balls and store them uncooked in the fridge. I used to bake them at the start of the week, but we quickly found that they would disappear extremely quickly when they were sitting on the counter. On the other hand, cold cookie dough is extremely tempting as well. You can also freeze the balls (hee hee) on a parchment-lined plate for a few hours. Transfer them to a freezer-bag and they’ll store for months. They won’t last in anyone’s freezer that long, but hypothetically it will work. You can bake them frozen, or transfer them to the fridge prior to baking. To avoid heating up my house for just a few cookies, I bake them in my convection/toaster oven. Make sure you cover your baking sheet with parchment to save yourself some dishes. Because I know you, and you don’t want to do dishes.

Whether you need a hearty after-school snack, or a bribe worthy of keeping two punk boys in check, this is the best whole wheat chocolate cookie recipe around. Despite what all those other recipes online say. 🙂

Making this recipe or others?

Post a photo on my Facebook page, share it on Instagram, or save it to Pinterest with the tag #sustainablecooks. I can't wait to see your take on it!

best chocolate chip cookies
5 from 2 votes
Whole Wheat Chocolate Chip Cookies
Prep Time
25 mins
Cook Time
10 mins
Total Time
35 mins

These are the softest whole wheat chocolate chip cookies you'll taste. Described as "more chocolate than cookie", you'll be amazed at how delicious whole wheat can be.

Course: Dessert
Cuisine: American
Servings: 18
Author: Sarah
  • ½ cup 1 stick butter, melted
  • ¼ cup white sugar I use organic
  • ½ cup brown sugar see the notes for a homemade version
  • 1 egg room temperature
  • 1 tsp vanilla see the notes for a homemade version
  • Pinch of salt
  • 1 tsp baking soda
  • 2 tbsp vital wheat gluten
  • 1 ½ cup whole wheat pastry flour
  • 2 cups semisweet chocolate chips
  1. Melt the butter in a microwave safe bowl. Allow it to cool for about 10-15 minutes. Do not skip this step!
  2. Add the white sugar and brown sugar, and mix,
  3. Add the egg and vanilla. Mix.
  4. Add the salt, baking soda, vital wheat gluten, and flour. Mix.
  5. Add the chocolate chips. Mix.
  6. Place the bowl in the refrigerator for 15-20 minutes. Do not skip this step!
  7. Preheat the oven to 350 degrees. Place rounded balls of dough on a parchment-lined baking sheet. Bake for 10 minutes. They’ll look pretty underbaked. Allow to rest on the pan for 10-15 minutes.
Recipe Notes

You’ll want to make sure you follow the instructions on allowing things to cool along the way. It’s annoying to wait the extra time, but it’s so worth it. By cooling the butter and then the batter, you don’t have to use extra flour to bind everything together.

Add the ingredients in the order in which they are listed in the recipe and in the instructions. 

Try making your own vanilla extract for an extra special flavor. 

And homemade brown sugar adds a special depth of flavor that makes these cookies extra special.

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These are the softest whole wheat chocolate chip cookies you'll taste. Described as

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11 comments on “Whole Wheat Chocolate Chip Cookies”

  1. I love your humor. I will have to try this recipe. After I buy some more chocolate chips. Of course, I still have M&M’s. Hmmmm…

  2. Purchased a Grain Maker grain mill last month and today received my first order of wheat berries from Azure. (Both of these events are partly your fault…specifically the Azure part) and am so excited about grinding our own flour and other grains to make our own chicken and sheep feed. However, I am a bit freaked out about switching my tried and true family favorite bread, cake, cookies, pasta recipes to whole wheat form. Do you add vital wheat gluten to all the baked goods??? Do you ever sift the flour repeatedly to make it more like a traditional white flour??? Inquiring minds (MINE) want to know…really.

    • Welcome to the dark side!!
      So, I have sifted the flour in the past but stopped because it didn’t make that big of a difference. I still buy a bag of AP flour from time to time and go through a bag of bread flour every month (for communion bread I make for church). For anything with whole wheat, I add 1 tbsp of vital wheat gluten per cup of flour. It makes the flour act a bit more like AP flour.

      With any of your favorite recipes, I would start small. I would try 25% whole wheat, to 75% “normal” flour. See how that works out and what you may need to adjust. As you get more comfortable using it, you can increase the whole wheat until you feel like you’ve achieved the results you want. Be ok with failing a few times, because it happens to any baker using a new ingredient.

      When baking with whole wheat, if the recipe calls for baking powder, I tend to amp it up a bit in addition to adding the vital wheat gluten.

  3. I have to make these! I also want to make the vanilla extract. How long will the extract keep once it is made?

  4. Is the wheat gluten necessary?

    • If you use whole wheat, it will give your cookies the soft and fluffy texture that most people want in a cookie. If you use normal flour, you can leave it out.

  5. I made these cookies Saturday night & though the recipe process is a bit odd, I will suck it up & make these again because they were utterly delicious & a big hit all around!!! Thanks for the great recipe.

  6. These were amazeballs. Fluffy and delicious (wholewheat!), more chocolate than cookie. Thanks for the recipe. 

    • So glad you liked them Steph! I can make those cookies in my sleep and even I am still surprised at how fluffy they are considering they’re whole wheat!