These vegan whole-wheat chocolate chip cookies will simply amaze you! A classic cookie with a healthier twist by using whole wheat flour and flax seeds instead of egg.

A top view of vegan whole wheat chocolate chip cookies on a cookie sheet.

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Why make this recipe

These whole wheat chocolate chip cookies are soft and chewy with a nice texture and a slightly nutty flavor. If you have never made cookies with whole wheat flour before, I think that you’re going to be amazed at how good they taste!

My mother used to make chocolate chip cookies with whole wheat flour occasionally when I was a kid. I knew that they were supposed to be healthier, but I always thought that they tasted better too. I still make traditional vegan chocolate chip cookies or double chocolate chip cookies, but these whole-wheat cookies are always my favorite.

Ingredients and substitutions

  • Vegan Butter – A high-quality vegan butter that comes in a stick will give you the best results with your cookies. You can use the stick version of my homemade vegan butter, Earth Balance sticks, Country Crock plant-based sticks, or Miyoko. If you don’t have any of these, you can use Earth Balance tub butter or even coconut oil. You want to avoid cheap brands of margarine that have too much water content in them.
  • Organic Brown Sugar – (the organic sugar is vegan) You can also use coconut sugar or Sucanat. These sugars have molasses in them and give you a softer cookie and great flavor. You can also use white granulated sugar or half white and half brown.
  • Vanilla Extract – for flavor.
  • Vegan Egg Replacer – I like to use ground flax seeds mixed with water as the egg replacement in this recipe. The grainy texture and slightly nutty taste pair well with the texture of the whole wheat flour. If you want to use something different see my guide to vegan egg replacement in baking.
  • Flour – whole wheat flour is what makes these cookies great! I use all whole wheat, but you can use half whole wheat and half regular flour if you would like.
  • Corn Starch – this is the key to making soft cookies! Just a little cornstarch produces an amazing texture. You can use potato starch as well. If you want a crunchy cookie, swap out the cornstarch with whole wheat flour.
  • Baking Soda – This makes your cookies rise and give them a chewy texture. (There is no need for baking powder in this recipe.)
  • Salt – you can reduce the amount, but don’t leave it out completely or the cookies will taste very bland. You may also want to sprinkle the tops with some coarse salt or flaky sea salt.
  • Vegan Chocolate Chips – you can use any brand of vegan chocolate chips that you want. You can find Enjoy Life brand at many major grocery stores or there are many other brands that are unexpectedly vegan like Trader Joe’s semi-sweet chocolate chips or the Belgian dark chocolate chunks from Aldi.

Helpful tools

  • An electric mixer is helpful but not required. (You can mix it with a wooden spoon if you don’t have a mixer, you just need to stir it a lot.)
  • Cookie sheet for baking your cookies.
Vegan whole wheat chocolate chip cookies cooling on a cookie wrack.

How to make vegan chocolate chip cookies

A full printable version of this recipe with ingredient measurements is available at the bottom of this post.

Step 1 – Take your butter out of the fridge about 1 hour before baking to allow it to come to room temperature or place it in the microwave for about 10-15 seconds to warm it a little. Preheat your oven to 375° F (190° C).

Step 2 – Mix together 1 tablespoon of ground flax seeds with 2 tablespoons of water and set aside for at least 5 minutes. (You can also use any other vegan egg replacement equal to 1 egg.)

Step 3 – With an electric mixer, cream the butter and brown sugar for 1 minute until fluffy. Then add 1 teaspoon of vanilla extract, and flax egg replacer mixture, and cream for an additional minute.

Step 4 – Turn off the mixer and add the flour mixture (flour, corn starch, baking soda, and salt) and mix on low until a thick dough is formed.

Step 5 – Add 1/2 cup of vegan chocolate chips and stir well. (At this point you can chill the dough and bake it up to 3 days later.)

Step 6 – Use a 1-tablespoon cookie scoop to spoon balls of cookie dough onto an ungreased baking tray. (You can also place a piece of parchment paper on the baking sheet for easy clean-up.)

Step 7 – Place a few more additional chocolate chips on the top of the dough ball to make your cookies look pretty.

Step 8 – Bake at 375° F (190° C) for 8-10 minutes until they have flattened and are just slightly brown. They will still look pretty soft and doughy, but that’s okay, they will firm up when cooled.

Removing vegan chocolate chip cookies from a cookie sheet.

Step 9 – Allow cooling for about 5 minutes on the cookie sheet before moving to a flat surface. Sprinkle with some coarse salt after they are baked if desired.

Pro Tips

  • Measure carefully! Even small changes to the measurement can make a big change in the outcome of your cookies.
  • Your dough should be very firm and hold its shape when spooned onto the cookie sheet.
  • If you want a firmer, crispier cookie, replace the cornstarch with 2 tablespoons of whole wheat flour.
  • Make sure your butter is soft before you start. You can also use melted butter if you wish, but it will give you a chewy fudgy texture like in my fudgy vegan chocolate cookies.

Storing your cookies

  • Countertop – Store the vegan whole wheat chocolate chip cookies in a sealed container for up to 3 days on the countertop or 1 week in the refrigerator.
  • Freezer – freeze the chocolate chip cookies in an airtight container for up to 3 months. Thaw by keeping it at room temperature for a few hours.
A top view of vegan chocolate chip cookies made with whole wheat flour cooling on a cookie wrack.

More vegan cookies

I love baking cookies and I have a ton of vegan cookie recipes on my site, but here are a few of my family’s all-time favorites.

A cookie sheet filled with vegan whole wheat chocolate chip cookies.
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5 from 1 rating

Vegan Whole Wheat Chocolate Chip Cookies

A classic tasting vegan chocolate chip cookie recipe made with whole wheat flour.

Ingredients

Egg replacer

  • 1 tablespoons ground flax seeds
  • 2 tablespoons water

Wet ingredients

Dry ingredients

  • 1 cup whole wheat flour
  • 2 tablespoons corn starch
  • 1/2 teaspoon baking soda
  • 1/2 teaspoon salt
  • 3/4 cup vegan chocolate chips

Instructions
 

  • Take your butter out of the fridge about 1 hour before baking to allow it to come to room temperature or place it in the microwave for about 10-15 seconds to warm it a little.
  • Preheat your oven to 375° F (190° C).
  • Mix together 1 tablespoon of ground flax seeds with 2 tablespoons of water and set aside for at least 5 minutes. (You can also use any other vegan egg replacement equal to 1 egg.)
  • With an electric mixer, cream the butter and brown sugar for 1 minute until fluffy. Then add 1 teaspoon of vanilla extract, flax egg replacer mixture, and mix for an additional minute.
  • Turn off the mixer and add the flour, corn starch, baking soda, and salt and mix on low until a thick dough is formed.
  • Add 1/2 cup of vegan chocolate chips and stir well. (At this point you can chill the doug and bake up to 3 days later.)
  • Use a 1 tablespoon cookie scoop to spoon balls of cookie dough onto an ungreased cookie sheet.
  • Place a few more additional chocolate chips on the top of the dough ball to make your cookies look pretty.
  • Bake at 375° F (190° C) for 8-10 minutes until they have flattened and are just slightly brown. They will still look pretty soft and doughy, but that's okay, they will firm up when cooled.
  • Allow cooling for about 5 minutes on the cookie sheet before moving to a flat surface or a cookie rack.
  • Sprinkle with some coarse salt after they are baked if desired.

Notes

  • Your dough should be very firm and hold its shape when spooned onto the cookie sheet.
  • If you want a firmer crispier cookie, replace the cornstarch with 2 tablespoons of whole wheat flour.
Serving: 1cookie, Calories: 114kcal, Carbohydrates: 15g, Protein: 1g, Fat: 6g, Saturated Fat: 2g, Polyunsaturated Fat: 1g, Monounsaturated Fat: 2g, Trans Fat: 0.02g, Sodium: 124mg, Potassium: 34mg, Fiber: 1g, Sugar: 9g, Vitamin A: 216IU, Vitamin C: 0.002mg, Calcium: 16mg, Iron: 1mg
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