Whole Wheat Chocolate Chip Cookies with Oats

Cookies, text overlay reads

A healthier spin on the original, whole wheat chocolate chip cookies are everything you want in a cookie: a little chewy, a little crispy and a lot decadent.

Recipe Overview

Why you’ll love it: For a chocolate chip cookie, these are pretty healthy with whole wheat flour and oats, and they taste great!

How long it takes: 15 minutes to make the dough, 10 minutes to bake each batch
Equipment you’ll need: electric mixer (optional), large bowl, cookie sheets
Servings: makes 5 dozen, depending on size

Layers of whole wheat chocolate chip cookies.

He loves the original crispy chocolate chip cookies and my chewy chocolate chocolate chip cookies (they’re my favorite!) but he’s always open to trying something that is a little better for him.

Don’t get me wrong, these cookies are still a treat!  They are chocolate chip cookies after all.  I try to focus on small changes, like making the cookies with whole wheat flour and oats, changes that can add up and make a difference in our health. Deprivation is not the answer, at least not for me.

I like to keep a big batch of this dough in the freezer. Ben will bake a couple in the toaster oven when he’s craving a chocolate chip cookie. Sometimes I even bake a small batch for him. Or for myself. Or sometimes we just eat the frozen dough.

About This Recipe

This is a basic chocolate chip cookie recipe but instead of regular all-purpose flour, you’ll be using whole wheat flour. The nutrition is amped up even more with a cup of oats.

Why make cookies with whole wheat flour and oats? Both are healthy whole grains that add fiber, protein, vitamins, and minerals to your diet. I often use at least half whole wheat flour to make cookies, if not all.

You’ll maybe notice that your cookies are a bit denser and have more of a grainy, almost nutty flavor. Quite possibly, you may not notice any difference at all; it’s very subtle. My family is used to whole wheat and they really never notice anything different. So I say, why not slip in a bit of extra nutrition when you can? Even in a cookie!

This dough does not need to be chilled before baking. If you want to chill it and bake the cookies later, that’s totally fine, too. We tested the cookies both ways and either way works.

Cookies on a white background.

I’ll get you started on the recipe here and give you some nice tips. As always, keep reading or hit the recipe button for the printable recipe near the end of the post. It has complete instructions, measurements, and nutrition information.

What You’ll Need

  • Whole Wheat Flour: Because whole wheat flour contains all the parts of the wheat kernel (bran, germ, and endosperm), it can spoil more quickly. It should be stored in the refrigerator or freezer. Wondering what you’ll do with the rest of the whole wheat flour? Try making whole wheat pancake mix or whole wheat banana bread. You’ll find lots more whole wheat recipes on my site.
  • Oats: Choose either quick oats or old-fashioned oats. I usually use quick oats for these cookies because they aren’t quite as noticeable as whole oats. Don’t use instant oatmeal or steel cut oats (Irish oats).
  • Chocolate Chips: You’ll need one 12 ounce bag of chips. I like to buy semisweet chocolate chips but milk chocolate chips are fine too if you prefer them.
  • Butter: Unsalted butter is the best choice for baking. Take it out a couple of hours ahead of time so it has time to soften. Rock hard chilled butter will be impossible to blend in. Butter spreads are not a good choice for making cookies; they contain too much oil.
  • Brown Sugar and Granulated Sugar: These cookies call for a combination (50/50) of both kinds of sugar.
  • Eggs: A couple of eggs add extra flavor and nutrition.
  • Baking Soda, Salt: Common cookie ingredients that add leavening and seasoning.
  • Vanilla Extract: This baker’s friend enhances the flavor of the cookies with warm vanilla undertones.
Ingredients needed for recipe, including whole wheat flour and chocolate chips.

How To Make This Recipe

If you plan on baking the cookies right away, turn your oven on to preheat. Line a couple of cookie sheets with parchment paper (for easy clean-up).

You’ll need a large mixing bowl. Begin by creaming together the butter, sugar, brown sugar, and vanilla. You can use a hand mixer or a stand mixer, or you can do it with good ol’ arm power. The mixture should be creamy and well-blended.

Butter and sugar creamed together.

Blend in the eggs until they are completely incorporated.

Eggs blended into milk and sugar.

Measure out the flour by spooning it into a measuring cup and leveling it off with a straight edge, like a table knife. Avoid scooping the flour out of the container with the measuring cup or shaking it down to level it. This will result in too much flour being added to your cookies and they’ll be tough.

Add the flour, baking powder and salt to the bowl.

Dry ingredients being mixed.

Mix those three ingredients lightly right on top of the butter mixture until they are blended; then stir them in. Keep stirring the dough until there’s no dry flour but don’t overstir.

Dry ingredients being blended in.

Once the flour is blended into the butter/sugar mixture, fold in the the oats.

Oats added to cookie dough.

Next, fold in the the chocolate chips until they are evenly distributed.

Chocolate chips added.

Use a tablespoon or scoop to portion out the dough onto the cookie sheets. Leave a couple of inches between the cookies because they will spread a little.

Unbaked cookies on baking sheet.

Bake the cookies in the preheated oven for about ten minutes or until they are golden brown. They’ll be slightly soft in the middle. The longer you bake them, the crisper they’ll be.

Baked cookies on sheet pan with chocolate chips sprinkled around.

Cool the cookies a few minutes on the cookie sheet until they firm up a bit and then transfer them to a wire cooling rack to cool completely.


Does whole wheat flour make cookies taste different?

You’ll maybe notice that your cookies are a bit denser and have more of a grainy, almost nutty flavor. Quite possibly, you won’t notice any difference at all; it’s very subtle. My family is used to whole wheat and it’s really not a big deal. So I say, why not slip in a bit of extra nutrition when you can? Even in a cookie!

Can you substitute all-purpose flour for whole wheat flour?

If your recipe calls for whole wheat flour, it’s usually okay to substitute all-purpose flour. That holds true for this chocolate chip cookie recipe and most other recipes. The cookies won’t be exactly the same but will taste great either way.

Make It Your Own

  • Not a fan of whole wheat flour? Feel free to use all-purpose flour instead!
  • There are some good gluten-free flours that can be substituted 1:1 for wheat flour. Note: I haven’t tested this recipe with gluten-free flour.
  • Feeling nutty? Substitute a cup of chopped nuts for the oats.
  • There are lots of baking chips to choose from: peanut butter, toffee, milk chocolate, butterscotch, etc. Mix things up a little by using a different flavor.
  • Rather have M&Ms? Try my popular M&M cookies!
Two cookies stacked, one with a bite removed.

Make-Ahead Ideas

The cookie dough can be made ahead and either refrigerated or frozen. The dough will keep in the refrigerator for two to four days, or in the freezer for up to two months.

I like to freeze the dough in convenient cookie sized amounts. Freeze individual dough balls for an hour or so on a tray until they firm up; then place them in a freezer safe container. You can take out as many as you like whenever you’re craving fresh warm cookies.

Storage Tips

Baked cookies, once they are thoroughly cooled, can be stored in an airtight container on the counter for up to a week. They freeze well too, and will keep for a few months.

Leftover Love

Is there such a thing as leftover cookies? I don’t think so! If you seem to have an excess of cookies and you don’t want to freeze them, make a chocolate chip cookie milkshake or simply crumble a cookie on a bowl of ice cream for a special treat.

More Cookie Recipes

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Did you make this? Be sure to leave a review below and tag me @rachelcooksblog on Facebook, Instagram, or Pinterest!

Two whole wheat chocolate chip cookies, one with a bite out of it.

Prep Time: 15 mins

Cook Time: 10 mins

Total Time: 25 mins

60 cookies

Prevent your screen from going dark

A healthier spin on the original, whole wheat chocolate chip cookies are everything you want in a cookie: a little chewy, a little crispy and a lot decadent.


  • Preheat oven to 365°F. Line cookie sheets with parchment paper.

  • In the bowl of a mixer (or you can mix it by hand), cream together butter, granulated sugar, brown sugar, and vanilla extract. Once creamy and fluffy, beat in eggs.

  • Add flour, baking soda and salt to bowl. Stir just enough to mix the dry ingredients, then mix into the butter mixture until just combined. Stir in oats, then chocolate chips.

  • Scoop onto cookie sheet (1 ½ tablespoons each), leaving some space between each cookie.

  • Bake for 10-11 minutes or until golden brown but still slightly soft in the middle. Cool on cookie sheet for five minutes, then transfer to a wire rack to cool completely.


  • If you prefer, substitute all-purpose flour, or use a combination of whole wheat flour and all-purpose flour.
  • A cup of chopped nuts can be substituted for the oats.
  • Dough can be refrigerated for two to four days or frozen up to two months to bake later. See Make-Ahead Ideas (above) for tips on freezing dough.

Nutrition Information

Serving: 1cookie, Calories: 104kcal, Carbohydrates: 13g, Protein: 1g, Fat: 6g, Saturated Fat: 3g, Polyunsaturated Fat: 1g, Monounsaturated Fat: 2g, Trans Fat: 1g, Cholesterol: 14mg, Sodium: 51mg, Potassium: 62mg, Fiber: 1g, Sugar: 7g, Vitamin A: 106IU, Calcium: 10mg, Iron: 1mg

This website provides approximate nutrition information for convenience and as a courtesy only. Nutrition data is gathered primarily from the USDA Food Composition Database, whenever available, or otherwise other online calculators.

Did You Make This?Be sure to upload a photo & tag me at @RachelCooksBlog. I love seeing what you made!

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