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Whole Wheat Chocolate Chip Cookies Recipe

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4.94 from 46 votes
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These Healthy Whole Wheat Chocolate Chip Cookies are loaded with whole wheat flour, a touch of brown sugar, coconut oil, egg, and dark chocolate chips. Reduced sugar. No butter. Still delicious. You’re gonna love ’em!

Whole wheat chocolate chip cookie sandwich with bite taken out

If you love this healthier treat, you should also check out: whole wheat oatmeal chocolate chip cookie bars, peanut butter energy bites, and healthy zucchini cake. 

Sometimes you just need a hot and gooey, fresh outta the oven, chocolate-y chip-y, cookie.

Ok. I lied.

You ALWAYS need a hot and gooey, fresh outta the oven, chocolate-y chip-y, cookie.

But sometimes.

You’re also trying to eat healthy…or at least healthy…er.

But you still need that cookie, amiright?!

Whole wheat chocolate chip cookies stackedThat’s why today, I made you guys whole wheat chocolate chip cookies.

This is a riff off my favorite chocolate chip cookie, but I made it healthier by…

  • replacing all-purpose flour with whole wheat
  • butter with coconut oil
  • milk chocolate chips with dark chocolate
  • significantly reduced the amount of sugar

But they still taste really really good.

You’re gonna love ’em.

Promise.

Chocolate chip cookie heldLet’s first address the elephant in the room.

Does whole wheat flour make cookies taste different?

I mean. Yes. But I don’t think that that’s a bad thing.

Whole wheat flour will give your cookies a more “earthy” flavor.

But honestly. I hardly notice a difference.

Some people might be able to taste more of a difference, but honestly, Trevor and I really couldn’t taste a difference.

Ingredients in low sugar healthy whole wheat chocolate chip cookies:

The ingredient list for these cookies is SO short. Which is great, because that means you probably already have these ingredients on hand!

  • Brown sugar
  • Coconut oil
  • Vanilla extract
  • Egg
  • Whole wheat flour
  • Baking soda
  • Salt
  • Dark chocolate chips
  • Maldon sea salt, optional but highly recommended

How do you make whole wheat cookies with coconut oil?

These whole wheat chocolate chip cookies are so quick to whip up.

  1. Use your hand mixer to cream together brown sugar, melted coconut oil, vanilla, and an egg
  2. Beat in whole wheat flour, baking soda, and salt
  3. Stir in dark chocolate chips
  4. Scoop cookie dough using a large cookie scoop
  5. Bake cookies on a silicone mat lined baking sheet in preheated oven at 350 degrees F for 8 minutes
  6. Sprinkle with maldon sea salt
  7. DEVOUR

Chocolate chip cookies held

Pro tip
It’s really easy to overmeasure whole wheat flour and make really dense and dry cookies. To avoid that, spoon the flour into a measuring cup and level it off with a knife.

Most of the time, when I’m baking, I just gently scoop out of the bag and shake to level, but with whole wheat flour, I find it better to spoon the flour into the measuring cup and leveling it off with a knife. 🙂

Even with these healthy swaps, I’m telling you, I really don’t think you’ll be able to tell the difference.

These cookies are SO soft and gooey and are still plenty sweet and chocolate-y.

Who’s ready for some hot and gooey, fresh outta the oven, chocolate-y chip-y, cookies?! 🙂

Whole wheat chocolate chip cookie ice cream sandwich with bite taken out abovePass the milk! Or scoop of ice cream. 😉

– Jennifer

These Healthy Whole Wheat Chocolate Chip Cookies are loaded with whole wheat flour, a touch of brown sugar, coconut oil, egg, and dark chocolate chips. Reduced sugar. No butter. Still delicious. You're gonna love 'em! showmetheyummy.com #wholewheat #chocolatechip #cookies

Whole Wheat Chocolate Chip Cookies

4.94 from 46 votes
These Healthy Whole Wheat Chocolate Chip Cookies are loaded with whole wheat flour, a touch of brown sugar, coconut oil, egg, and dark chocolate chips. You're gonna love 'em!
Prep Time: 10 minutes
Cook Time: 8 minutes
Yield: 12 cookies
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Ingredients

US Customary - Metric
  • ½ cup brown sugar packed
  • ½ cup melted coconut oil
  • ½ tablespoon vanilla extract
  • 1 large egg room temperature
  • 1 ¼ cups + 2 tablespoons whole wheat flour spoon and level to measure (see notes in post above)
  • ½ teaspoon baking soda
  • ¼ teaspoon salt
  • ½ cup dark chocolate chips
  • Maldon sea salt for topping

Recipe Video

Instructions

  • Pre-heat oven to 350 degrees F and line a baking sheet with a silicone baking mat. Set aside.
  • In a medium sized bowl, use a hand mixer to cream together brown sugar, coconut oil, vanilla, and egg.
  • Beat in whole wheat flour, baking soda, and salt.
  • Stir in chocolate chips.
  • Use a large cookie scoop to scoop cookie dough onto prepared baking sheet.
  • Bake in preheated oven for about 8 minutes.
  • Remove from oven and top with a sprinkle of maldon sea salt.
  • Cool slightly and serve!
  • Optional - serve as ice cream sandwiches!
  • Take 5 seconds to rate this recipe below. We greatly appreciate it!
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STORING
Room Temp:1 Week
Refrigerator:2 Weeks
Freezer:3 Months
Reheat:Microwave until warmed
*Storage times may vary based on temperature and conditions

Notes

These make large cookies, feel free to make smaller cookies to reduce calories. 

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Nutrition Information

Nutrition Facts
Whole Wheat Chocolate Chip Cookies
Amount Per Serving
Calories 204 Calories from Fat 108
% Daily Value*
Fat 12g18%
Saturated Fat 10g63%
Cholesterol 15mg5%
Sodium 110mg5%
Potassium 112mg3%
Carbohydrates 22g7%
Fiber 1g4%
Sugar 11g12%
Protein 2g4%
Vitamin A 25IU1%
Calcium 37mg4%
Iron 0.7mg4%
* Percent Daily Values are based on a 2000 calorie diet.

*Note: Nutrition information is estimated and varies based on products used.

Keywords: easy, healthy, whole wheat flour
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Course: Dessert
Cuisine: American

Reader Interactions

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  2. Erin

    Oakland, California

    5 stars never thought I’d learn to love whole wheat cookies but this recipe is super tasty and easy. I make with real unsalted butter (just my preference) mini semi-sweet chocolate chips. Also make them mini cookies, so I get 2 dozen small cookies, 2 of them = about 215 calories. Love that I can make “healthier” cookies at home, they’re really good paired with some vanilla ice cream. about to make some keto vanilla in my mini ice cream maker today:) bon appetite!
    Reply

    • Erin

      Oakland, California

      oops, I forgot another modification: instead of those last 2 TBLS of whole wheat flour, I sub 1 TLBS coconut flour. I’ve found in my cookie recipes, the coconut flour really helps fluff up the cookie. Otherwise a lot of times my cookies turn our flat & crispy but I like the soft, melt-in-your mouth cookies & this does the trick!

  6. Kyle

    5 stars Easy recipe. I love the whole grains, and the less sugar. Now I can eat more without a tummy ache. Very tasty! Thank you.
    Reply

    • Jennifer @ Show Me the Yummy

      Honey should be fine, but since it’s a different consistency, I can’t guarantee the results 🙂

  13. Anonymous

    India

    5 stars Made this an hour back, 7:30 pm India time. My four year old has been eating it almost non stop. He’s with the fifth cookie now. Absolutely delicious, super easy and quick to make.. Thank you.
    Reply

  14. Fern

    Plainview, New York

    5 stars This chocolate chip recipe was very easy to make and you will not be disappointed when you are done. Very tasty and delicious. I highly recommend it for those who are more health conscious!
    Reply

  19. Kate

    Sarasota, Florida

    5 stars Katie from Glen Cove: Thank you – I have LPR and will try this recipe because of your comment! Anyone suffering from Reflux of any kind, read Dr. Aviv’s book, Killing Me Softly From Inside.
    Reply

  21. Jessica

    Orlando, Florida

    5 stars I have made this a few times and double the recipe and use maple syrup in place of the brown sugar for one batch. This is my go to recipe now! It is so yummy! Thanks for this recipe!
    Reply

  30. Louise

    United States

    4 stars These are easy to make. Flavor is nice and not too sweet. Should the batter be crumbly? It was difficult to shape the dough.
    Reply

    • Jennifer @ Show Me the Yummy

      Hi, Louise! I’m glad you loved the flavor. If you batter was dry, I’m wondering if you over measured your flour. Did you spoon and level it rather than just scooping with the measuring cup? If it gets too packed in there may end up being too much which can result in dryer batter. Hope that helps!

  31. Kate

    Glen Cove, New York

    5 stars I REALLY loved the flavor but they were a bit cakier than I wanted them to be. Was that me or the recipe? I swapped the brown sugar for maple syrup (did 1/3 as maple syrup is not 1:1 with sugar). I mixed by hand as well. Any insight? Also can I freeze the dough for another time? How long can it stay in the fridge?
    Reply

    • Jennifer @ Show Me the Yummy

      Hi Kate! So glad you loved the flavor. 🙂 I’m guessing it’s because you used maple syrup instead of brown sugar and used less than what was called for! You also maybe have over measured your flour, which is easy to do with whole wheat! If you can find it, whole wheat pastry flour is my favorite! It’s lighter than “regular” whole wheat. The dough would freeze great! Freeze the scoops on a baking sheet first, then place the frozen dough balls into a ziplock baggie! How long can what stay in the fridge? The dough? The cookies?

    • Katie

      Glen Cove, New York

      Soooo helpful!! I’ll def try the whole wheat pastry flour next time. Oh and I meant how long can the dough stay in the fridge. And once again… THANK YOU. I’m on such a strict diet for acid reflux and this recipe (had to use carob chips) is saving my holidays from being sad and cookie-less! The salt is just the greatest thing ever lol.

    • Jennifer @ Show Me the Yummy

      Dough can stay in the fridge for 2-3 days! 🙂 And you’re so welcome! Glad to be helpful and I’m SO glad your holidays aren’t sad and cookie-less now! Glad we’re on the same page when it comes to the salt! 😉

  32. Maddy

    Pittsburgh, Pennsylvania

    5 stars Delicious! I’ve made these twice, once with some reese’s candies left over from halloween and another time with some dark chocolate. They taste great and aren’t too sweet. The only change I made was that I used vegetable oil rather than coconut oil.
    Reply

    • Vanessa

      United States

      4 stars I’m making these right now. Used a small scoop to put them on the sheet. 8 minutes of baking time has not been nearly enough. What do you think that’s about?

    • Jennifer @ Show Me the Yummy

      Your oven probably runs colder than mine does! Use an oven thermometer to check 🙂

  33. Sushree

    Bengaluru, Karnataka

    5 stars This is perfect gluten free cookies. I replaced coconut oil with butter and choco chips with dry fruits. It still turned out Yummy
    Reply

  35. Lisa

    Venice, Florida

    5 stars This the perfect cc cookie finally a lower sugar cookie with REAL sugar not the fake stuff that makes me sooo sick! And being a lot less sugar you’d think it wouldn’t be yummy but nope delish and satisfying all the way. It delivered everything the author of this recipe said it would!!! I’d give it 10 stars out of 5 if i could! Highly recommend. One thing I did change was I used grape seed oil instead of coconut oil since it’s not as high in saturated fat. Yummmmmmmy 😁😀😆will be my go to cc cookie recipe forever!
    Reply

    • Jennifer @ Show Me the Yummy

      I always recommend making the recipe as is for best results, but you could try replacing half the amount with applesauce!

  42. Leanne

    Edmonton, Alberta

    5 stars These are scrumptious! My tween daughter and I were looking for an easy recipe for cookies that we could drop off at my mom’s as a pick-me-up. This checked all the boxes! Thank you for sharing. PS. We followed the recipe word for word. We doubled the recipe and it yielded 30 medium-sized cookies. Enough to share but plenty left over for my family. 🙂
    Reply

  44. Will

    Nazareth, Kentucky

    5 stars These are delicious! I made them for my Mom, who is a chocoholic, but pre-diabetic, so we’re trying to keep the sugar down–only 11g sugar per serving. She described them as “decadent”, which is quite high praise from her. They are rich and gooey and fill the palate with flavor. The whole wheat flour actually amplifies the flavor of the chocolate with its warm, earthy tones.
    Reply

  45. Allison

    Las Vegas, Nevada

    5 stars Tried these with white chocolate chips and maple syrup instead of vanilla because that’s what I had in the house. They came out so yummy! I’d like to make them smaller next time–about half the size. Would I use the same cook time/temp?
    Reply

    • Jennifer @ Show Me the Yummy

      Hi Allison! Glad you loved these 🙂 I’d halve the baking time and add more time if necessary. Temp will remain the same!

  46. Bryan

    5 stars Ironically, I actually like the taste difference with whole wheat for some reason. When I was younger I use tried making whole wheat cookies, they didn’t turn out all that great though but then I got the hang of it haha
    Reply
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