whole wheat chocolate chip cookie

Whole Wheat Chocolate Chip Cookies

These whole wheat chocolate chip cookies are simple to make. Some claim they are the most wonderful vegan chocolate chip cookies ever! They bake thick and chewy on the inside, while being golden and crisp on the edges. This recipe is lower in sugar than most cookies, and the whole wheat flour adds more fiber and protein to this delicious vegan cookie recipe.

whole wheat vegan cookies cooling on a rack

To start making these cookies, preheat the oven to 375 degrees and get your sheet pans lined with parchment paper. Grab your bowl, measuring spoons and cups, ingredients, and your wooden spoon or stiff spatula.

By taking the steps to get all the ingredients and equipment in one place, you will be set up for a smoother cooking flow. In the restaurant biz, we would call this “mise en place”, a French term for “everything in its place”. We like to use this practice even cooking at home. Not only does this set yourself up for an easier recipe to make. It makes cleaning easier when you have all the ingredients in one spot. Once you’re finished measuring each ingredient, put them away as you finish.

Begin the recipe by creaming together the coconut oil, sugar, and vanilla. Make sure the sugar is well incorporated.

Next, add the flax eggs and the coconut milk, continue to still until fully incorporated.

After the wet ingredients are mixed together smoothly, add in the flour, baking soda, and salt. Stir until the dough forms together. The dough will be super thick!

Finally, fold in the chocolate chips to the dough. Mix until the chocolate is evenly distributed throughout the dough. The vegan cookie dough recipe is now ready for baking. Or eating if you desire, hehe.

How to Bake

Start by scooping 2-3 Tbsp sized scoops onto the cookie trays. Allow an inch or 2 between the cookies for even baking. Once all the cookie dough is scooped, press the mounds gently with the hands so that the cookies are a bit more flat.

These cookies are thick and do not flatten, so make sure not to skip this step, as you will end up with something more like dough balls instead of a traditional cookie. Place the cookies directly on the center rack in the oven.

Please note that these cookies can become very hard if you over bake them! It is always better to have a super soft cookie instead of a hard cookie if you ask us! We bake these cookies for 9 minutes and that seems to be the perfect time for us!

After cooling for 5+ minutes on the sheet tray, transfer to a wire rack and allow to cool for an additional 10 minutes. The cookies come out slightly soft, and stay that way for a couple days.

How to Store

When storing the leftover whole wheat chocolate chip cookies, it is important to store them in an airtight container. This is assuming that you have any leftovers! These cookies will stay fresh for about two days. After that the cookies begin to lose their moisture and become more firm. Which is still nice, but you will want them with a glass of milk.

You can make any modifications to these you like. Use walnuts, pecans, or almonds. Substitute white chocolate for dark, add macadamia nuts and you have an awesome vegan white chocolate chip macadamia nut cookie. The possibilities are endless!

If you tried one of our recipes or found our articles helpful, let us know in the comments below how it turned out!

Follow us on PinterestInstagram, and Facebook. Take a picture of your creations and tag us using #cookingupvegan.

Luna & Nate

Whole Wheat Chocolate Chip Cookies

Recipe by Cooking Up Vegan Course: DessertsCuisine: AmericanDifficulty: Easy


Prep time


Cooking time


Total time



Perfect vegan cookies made with whole wheat flour and loaded with chocolate chips.


  • 1/2 Cup 1/2 Coconut Oil, soft not melted

  • 3/4 Cup 3/4 Brown Sugar

  • 2 tsp 2 Vanilla Extract

  • 1/4 Cup 1/4 Coconut Milk

  • 1 1/2 Each 1 1/2 Flax Eggs

  • 2 1/4 Cup 2 1/4 Whole Wheat Flour

  • 1 tsp 1 Baking Soda

  • 1/4 tsp 1/4 Salt

  • 1 Cup 1 Chocolate Chips (dairy free)

  • 1 tt 1 Flakey Salt (optional)


  • Preheat the oven to 375 degrees and line 2 sheet trays with parchment paper.
  • Make the flax eggs and set aside.
  • In a large bowl, mix the sugar, vanilla, and coconut oil until fully incorporated.
  • Next, add the coconut milk and flax eggs. Mix together.
  • Add the flour, baking soda, and salt. Mix until a very thick dough forms. Fold in the chocolate chips.
  • Scoop out 3 Tbsp sized dough balls onto the cookie sheets. Lightly press the cookies down on the top to help them spread. Bake the cookies in the oven for 9-10 minutes.
  • Remove the cookies from the oven and place the flakey salt on the top. Allow to cool for a few minutes before transferring to a cooling rack.


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Nutrition Facts

18 servings per container

  • Amount Per ServingCalories203
  • % Daily Value *
  • Total Fat 11.3g 17%
    • Saturated Fat 8.3g 40%
    • Trans Fat 0g
  • Cholesterol 0mg 0%
  • Sodium 108mg 5%
  • Total Carbohydrate 24g 8%
    • Dietary Fiber 3g 12%
    • Sugars 108g
  • Protein 3g 6%

    * The % Daily Value tells you how much a nutrient in a serving of food contributes to a daily diet. 2,000 calories a day is used for general nutrition advice.


    1. A super easy way to make a healthier chocolate chip cookie.!These melt in your mouth…it’s hard to wait for them to cool.

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