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Make sure to read the tips in the post so your whole wheat cookies come out amazing every time!

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Whole Wheat Flour VS. Regular Flour Cookies
Will the chocolate chip cookies made with whole wheat flour taste any different than with regular white all-purpose flour? Yes, just like there’s a difference in bread cookies with only whole wheat flour are heartier.
You’ll find that they’ll taste delicious and some people swear that the whole-wheat version tastes better.
Whole-wheat flour is the entire wheat kernel ground up into flour, while white all-purpose flour is lighter and softer because the outer shell is removed before grinding.
The whole grain flour gives the cookies a whole grain, nutty taste- which I think we can all agree tastes amazing with melted chocolate chips, butter, and brown sugar.
Ingredients
One comforting fact about whole wheat chocolate chip cookies is the ingredients also happen to be basic pantry staples! The measurements are at the end of the post, but first, check the things you'll need:
- Butter: you’ll add it softened, not cold or melted.
- Sugar: I use the same amount of white and brown sugar for sweetness and moisture. More on this below.
- Eggs: to bind the ingredients.
- Vanilla extract: classic cookie flavor!
- Whole wheat flour: makes the cookie more nutritious than the ones made with regular flour.
- Baking soda: helps the dough rise.
- Salt: enhance all these delicious flavors.
- Semisweet chocolate chips: or you can use chocolate chunks instead.
Want to take it to the next level with lots of mix-ins? Try my epic Kitchen Sink Cookies next!

How to Make Whole Wheat Chocolate Chip Cookies
Everyone loves a moist, chocolate chip cookie recipe and good thing you are here because this is THE ONE! No frills or fancy stuff here, only simple ingredients and basic cookie-makin' techniques, so let's get to it. Here’s how to make whole wheat chocolate chip cookies step-by-step:
- Prep the oven
This is the time to preheat the oven and arrange the oven racks to accommodate baking one or two baking sheets. You’ll want to arrange them in the middle area. - Cream butter with sugar
Mixing these two is essential for the sugar to melt during baking. - Add the eggs and vanilla
Eggs will bind the dough and vanilla… well, are they even cookies without it? - Add flour and chocolate
Once you have the wet ingredients incorporated, you’ll add the flour to make the dough and mix the chocolate chips as the finishing touch. - Scoop the cookie dough
Using a large spoon or cookie scooper to form dough balls. - Shape them
With your hands, compact the dough into 1 ½-inch balls and place the cookies onto the lined baking sheets. Press down slightly to flatten. If you’re not baking all of them, you can freeze them after forming them into balls. - Bake
Chewy cookies need to be removed earlier, since all cookies harden when they cool. Baking time will vary on how thick the cookies are; they only spread slightly. - Cool down
When they’re ready, let them cool down a bit before biting into them; that is if you can wait that long.
Do I Need to Line the Baking Pan?
Absolutely. I personally feel strongly about this one because lining the pan ensures that the bottoms don’t burn. You can line a pan with parchment paper or a silicone mat.
Unless you own USA Pans. They claim that they don't need to be greased or lined and even though I own them myself, I still line the pan -I like to play it safe.
Tips to Make Chewy Cookies
My kids love "chewy" cookies. They prefer warm and chewy versus crunchy and dunking. These whole wheat cookies are chocolatey, chewy, gooey, and we want them to stay that way! Here's how to make the ultimate, most perfect, chocolate-y chippity cookies ever:
Reduce baking time
Most recipes call for 12 minutes in the oven, which seems like a great idea when you pull golden, brown cookies from the oven, but as they cool, they harden. However, baking the cookies until they are just starting to hold together, 8 -10 minutes, is the fastest route to a perfectly chewy cookie!
Warning: the cookies will look pale and puffy, but trust me, you want to do it this way. There's a difference between a "raw" cookie and a soft in the middle. You want the latter.
You'll know the whole wheat chocolate chip cookies are ready because the edges are solid and the dough isn't runny on the baking sheet. Give them some time to cool, then pick one up and take a bite. They'll still be chewy, gooey and so so soft *squeals.
Brown sugar
Brown sugar has a high moisture content, which makes it a great ingredient for soft, chewy, chocolate chip cookies! #missionaccomplished.
I prefer a 1:1 ratio of white to brown sugar. Some people swear by more white sugar, others by more brown. As long as the total sugar amount remains the same, you can tweak it to your preference. It's also the same reason we love it in this Chocolate Chip Banana Bread.
Softened Butter
You'll see many cookie recipes that call for softened butter, but what does that mean? Softened butter has sat at room temperature and is soft but not melted or liquidy. It should be slightly firm, but when pressed, your finger will leave an indention, not cause the whole stick to collapse.
Measure flour with the "scoop and swoop" method
One very important step for chewy chocolate chip cookies is measuring out your whole-wheat flour. Whole wheat flour, by default, is denser than white, all-purpose flour because it contains the grain's outer shell. It's essential you measure flour with the "scoop and swoop" method, as shown in the video below if you want to prevent your cookies from being too dense.
How to Store Whole Wheat Chocolate Chip Cookies
These cookies are going to disappear fast! That said, you can store leftover cookies in an airtight container on the counter for up to 3 days. Pro tip: you can add ½ slice of sandwich bread in the container to keep the cookies moist.
Can you Freeze these Chocolate Chip Cookies?
Yes! I usually prep the dough for 36 cookies and bake ⅓ of it to get 12 cookies. I freeze the other unbaked cookie dough balls in a zip bag for up to 3 months. Don’t forget to label the bag! This means warm, inviting chocolate chip cookies are always 10 minutes away. Amazing!
100% Whole Wheat Chocolate Chip Cookies

Ingredients
- 1 cup butter, softened
- ¾ cup white sugar
- ¾ cup brown sugar
- 2 large eggs
- 1 teaspoon vanilla extract
- 3 cups whole wheat flour
- 1 teaspoon baking soda
- ¾ teaspoon salt
- 1 ½ cups semisweet chocolate chips, or chunks
Instructions
Prep:
- Preheat the oven to 375F. If baking two cookie sheets at once, arrange the oven racks as close to the middle oven as possible. This recipe yields 3 dozen so you’ll need to line 3 baking sheets with parchment paper.
Make the cookie dough:
- In a large bowl or the bowl of a stand mixer, cream the butter, white sugar, and brown sugar together until smooth. Add the eggs and vanilla extract and mix until light and fluffy.
- To the creamed sugar mixture, add the whole wheat flour, baking soda, and salt. and mix to combine. Stir in the chocolate chips into the cookie dough.
- Use a large spoon to scoop out about 2 tablespoons of cookie dough, and using your hands, compact the dough into 1 ½-inch balls. This recipe will make approximately 3-dozen (36 cookies).
- Place the cookies onto the lined baking sheets, about 2 inches apart, and with your hands, press down slightly to flatten. I usually bake 1 dozen at a time.
Bake:
- Bake in the preheated oven for 8 to 10 minutes. This will vary on how thick the cookies are; they only spread slightly. Remove from the oven and allow the cookies to cool down slightly before removing from the baking sheet.
Store:
- Store leftover cookies in an airtight container on the counter for up to 3 days. Tip: add ½ slice of sandwich bread in the container to keep the cookies moist. You can also freeze unbaked balls of cookie dough in an zip bag for up to 3 months.







Hannah says
Delicious cookies using all whole wheat flour! Toddler approved
Robin says
Just ok.