These soft and chewy fresh milled chocolate chip cookies are made with 100% freshly milled wheat flour and stay tender—not dry or crumbly. If you’ve struggled with dense or dry whole wheat cookies, this recipe is designed to give you bakery-style results with incredible flavor and texture every time.

Chocolate Chip Cookies with Fresh Milled Flour

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If you don’t have fresh milled flour, you can use all purpose flour, you may just need to adjust the amount a little. You can buy fresh milled flour, or if you are ready to take the plunge, invest in a home mill. You can see mine in the video of my recipe.

Why These Fresh Milled Chocolate Chip Cookies Stay Soft

Fresh milled flour absorbs more liquid than all purpose flour, so this recipe was created with that in mind
Cornstarch was added to help create a tender cookie
Extra egg yolks add some extra richness
The blend of sugars helps create a tender center with crispy edges

Will my kids even eat fresh milled flour?

I remember when I first started milling my own flour at home I was a little worried about how it would affect my baking. Since I knew it wouldn’t taste exactly the same as all purpose flour, and didn’t totally know what to expect. I am happy to say, it was a pretty easy transition. I’ve been using fresh milled flour for about two years now, and my kids still happily eat my baked goods. It helps that cookies have lots of sugar in them, and these chocolate chip cookies with home milled flour are no different. They are for sure kid approved though! I was taking pictures and two of my girls popped over to give them a thumbs up.

soft fresh milled chocolate chip cookies

What are the Ingredients in Soft Whole Wheat Cookies?

Home milled flour: I really feel this helps the cookies taste fresher, with a slightly nutty flavor.

butter: unsalted, softened butter

sugar: both brown and white sugar are used to help them have the perfect texture of not too crispy and not too soft. Just think a soft center with crispy edges

egg and egg yolks: whole eggs help with binding, while yolks add to the texture as well as help add a richness

cornstarch: another ingredient that helps with chewyness and softness

baking soda and powder: both used to help leaven the cookies.

salt: to help add to the flavor

vanilla: once again adds to the flavor

chocolate: it is a chocolate chip cookie with fresh milled flour

These cookies really hit the spot, particularly when they are warm and gooey just after they have finished sitting on the cookie sheet. For these chocolate chip cookies with fresh milled flour I ended up using a combination of chocolate chunks and milk chocolate chips. Boy on boy do I like how they turned out. I’ve been a tried and true semisweet chocolate chip girl for a long time, but I think that may be changing.

chewy whole wheat chocolate chip cookies

I really think the home milled flour helps give these cookies an amazing taste. When I first made these cookies I would sift out a small portion of bran. But now, I don’t even bother doing that. These cookies are a great example of how 100% whole wheat chocolate chip cookies can still be soft, chewy, and full of flavor. If you are looking for other fresh milled flour recipes you can check out these banana chocolate muffins. You can also try this fresh milled sandwich bread.

If you have jumped on board the sourdough trend, check out my post on how to make sourdough using fresh milled flour. It’s a learning curve but very worth it. I also have lots of fresh milled flour discard recipes for you to try! These double chocolate cookies with sourdough discard are a big winner as are these chocolate chip cookies.

Tips For Baking Cookies with Fresh Milled Flour

Let the dough fully hydrate by chilling it for at least 30 minutes or up to an hour
Be sure to use soft wheat with baking cookies. That will give you more tender and chewy cookies
Consider investing in a scale for more precise measurements as using measuring cups can be unpredictable
Do not over bake, fresh milled flour can dry out faster than all purpose. This is why we pull the cookies out when they are just turning brown.

Frequently Asked Questions about Fresh Milled Cookies

How is Fresh Milled Flour Different than All Purpose?

It is important to note that overall, fresh milled flour behaves differently than all-purpose flour. Due to the higher bran content, it is “thirstier”, meaning it absorbs more water than all purpose flour. For cookies that means using less fresh milled flour than you would all purpose, or adding more liquid into your dough.

What Wheat Berries Should I Use in Fresh Milled Cookies?

I tend to stick with soft white wheat when making my cookies, as the lower protein content helps to make a more tender cookie. That being said feel free to experiment with different berries! There are so many tasty combinations that could be made.

Why Did My Fresh Milled Cookies Flatten Out?

Fresh milled flour needs more time to hydrate since it is “thirstier” than all purpose flour. By allowing it to chill in the fridge for at least 30 minutes, this lets the flour sufficiently hydrate before baking. You also need to make sure to use soft wheat berries and not mill your flour too coarse.

Do I Need to Sift the Flour?

You absolutely do not need to sift out any of the bran when making these cookies. I have made these cookies both ways, and they turn out amazing either way you bake them. Sifting out some of the bran will produce a slightly softer cookie, so if that is something important to you, then sift out a small amount of bran.

Can I freeze the dough?

Yes you can! After allowing the dough balls to chill for 30 minutes transfer them into a zip lock bag (or air tight container) and put in the freezer. When ready to bake simply take the dough out, place on a cookie sheet, and bake. I usually add 2-3 minutes more on the bake time since they were frozen.

Fresh Milled Cookie YouTube

If you like watching videos, you can check out my YouTube video here. Be gentle… I felt so awkward in front of the camera. But one of my goals is to do more YouTube, so I’ve got to practice. My blog has come a long way in the 10 years I’ve had it, and hopefully my YouTube skills will improve as well.