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Whole Wheat Chocolate Chip Cookies Recipe – A Healthy Alternative

Whole Wheat Chocolate Chip Cookies Recipe – A Healthy Alternative

Last Updated on 17th December 2021 by

Can anything really top the gooey, chocolatey goodness of chocolate chip cookies? I don’t think so, and this cookie is a staple of many a picnic, sporting event, cookout, and school lunch. It’s the dessert we all have in common- popular among kids and adults both.

If you have ever made chocolate chip cookies, then you realise how much sugar it has and how unhealthy it can be. All that gooey goodness comes at a price, unfortunately, and this is a cookie that is far from nutritious. I want to share with you a recipe for wholesome whole wheat chocolate chip cookies, and you can use that to make these tasty treats a bit healthier.

Of course, whole wheat means more fibre, which is great for your digestive system and for your heart health. It helps to get rid of things in your body that you shouldn’t have there, and it cleans out your colon for better overall health. Whole wheat is a very nutritious substitute for white flour, and that’s partly because of how the bleaching process that white flour undergoes gets rid of almost all of its nutritional value.

If you are looking for chocolate chip cookies with whole wheat flour in order to put a little nutritious value into your desserts, then I have you covered. I want to share my recipe that makes superb whole wheat chocolate chip cookies. They’re so good, you may not want to go back to the white flour ones again.

Can You Just Substitute Wheat Flour in for White Flour?

Keep in mind, of course, that I order to make the whole wheat flour work in these cookies and to attempt to make cookies that taste nearly identical to classic white flour chocolate chip cookies, some changes have to be made. You can’t just substitute out the white flour in the recipe you use for whole wheat flour and expect good results.

When making chocolate chip cookies whole wheat flour versions, you cannot just take your regular chocolate chip recipe and change the white flour to whole wheat, expecting good results. The whole wheat flour will decrease the rise of yeasted goods baked in the oven. How does this happen? It’s because whole wheat flour absorbs a lot of liquid- more than the white flour does. That results in a packed, harder, drier dough. You get a cookie that is tougher and not as moist as it should be. How are you going to get a gooey chocolate chip cookie from that recipe?

Well, you can’t, so the recipe has to change. I’m going to share with you my favourite way to make chocolate chip cookies whole wheat so that you can know ahead of time that it works and the recipe will make for good tasting cookies. You don’t have to play around with quantities and try a substitution to see what will work well. It has already been figured out for you.

Best Whole Wheat Chocolate Chip Cookies

With all that being said, let’s get into the recipe. I know you’re probably itching to try this out and see if this whole wheat chocolate chip cookies recipe really makes decent cookies.

Best Whole Wheat Chocolate Chip Cookies
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Best Whole Wheat Chocolate Chip Cookies


  • 2 cups of semisweet chocolate chips
  • ¾ cup of granulated sugar
  • 1 cup of softened butter (or margarine)
  • 1 egg
  • 1 tsp of vanilla
  • ¾ cup of packed brown sugar
  • ½ tsp of salt
  • 2 cups of whole wheat flour
  • 1 tsp of baking soda


  • Preheat your oven to 375 degrees Fahrenheit.
  • Combine vanilla, egg, butter, and both sugars in a large bowl.
  • Once those are combined, add in whole wheat flour, baking soda, and salt. This makes a stiff dough.
  • Add in chocolate chips, stirring until everything is combined.
  • Use a spoon or your hands to pull out small, round balls of cookie dough from the bowl and drop onto an ungreased cookie sheet, leaving about two inches between each one. Make sure to give the cookies enough space in order to spread out fully. You don’t want to stifle their spread.
  • Bake the cookies for about nine minutes. When done, they should be light brown and have soft centers. You can remove them immediately from the cookie sheet and place onto a wire rack to cool.

Make It Your Way

There are some great variations and additions to these cookies that you can try in order to make them the way you want or to tweak the recipe to try something different.

If you want chewy whole wheat chocolate chip cookies, this recipe works okay for that, but you can make them chewier. The way I do that is to alter the recipe just slightly and make whole wheat chocolate chip cookies with coconut oil for a chewier texture. This works wonders at making the cookies the right consistency for a truly chewy experience.

Another way to make them chewy is to alter the recipe slightly and use whole wheat pastry flour instead of simple whole wheat flour. Making whole wheat pastry flour chocolate chip cookies works with the same process as the recipe up above, but you do get chewier cookies. So, if you tried the recipe I gave you and where not completely satisfied with how chewy your cookies can out, try them as whole wheat coconut oil chocolate chip cookies or try the pastry flour variation. I think you will really like how they turn out.

You can also add in some other ingredients to make the cookies just the way you want them. For some added fibre, try making whole wheat oatmeal chocolate chip cookies. Just add in 2 cups of rolled oats and cut the wheat flour down to ¾ of a cup. In the oatmeal chocolate chip cookies whole wheat flour version, the oatmeal can take the place of some of the flour. The texture, consistency, and flavour of these is truly sensational, and I think you will be pleased with the way they turn out.

You could take out the egg and butter and make this a vegan whole wheat chocolate chip cookies recipe. How can you get the cookies to be chewy and to hold together without the butter and eggs? I just take those two things out and replace them with melted coconut oil. You can use other flavour neutral oils like avocado oil or extra virgin olive oil as well. The eggs simply aren’t necessary for these cookies, and the oils take the place of butter as a fat/liquid.

You can also try making white whole wheat chocolate chip cookies. Do this by using 50% all-purpose whole wheat flour and 50% white whole wheat flour. That will help to preserve the flavour and make these taste just right. You could simply change out the whole wheat flour in the recipe for white whole wheat flour, but the cookies will come out sweeter. If you don’t want that to happen, use the half and half method I just gave you.

You can also add in pecans for a satisfying crunch to your cookies or substitute the semisweet chocolate chips for white chocolate chips. Plenty of variations are available that won’t drastically alter the cookies and that can be used with the same recipe up above, so try a few things out and see what tickles your fancy.

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I'm Pauline, a mother of four grown children, my passion for cooking stemmed from the joy i get cooking for my family. I love to try new dishes, especially when dining out but creating and sharing my own recipes is my favourite thing to do!

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