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These fresh milled flour cookies taste nothing like traditional whole wheat cookies! They’re soft and chewy with a brown sugar flavor and pops of chocolate chips, yet are made with 100% whole-grain flour. You would never be able to tell!
After switching to freshly milled grains, I realized I needed to make a few changes to my favorite recipes.
Fortunately, these chocolate chip cookies require minimal adaptation. They’re soft and chewy with a nice bite on the edges and are heaven with a glass of milk!
The main difference is to double-grind the whole wheat flour until it’s super soft and fluffy. (Note: Not all mills are suited for this!)
Using white whole wheat also keeps the flavor really mild, allowing them to taste more like “regular” chocolate chip cookies instead of whole wheat ones. I served them to my family, and no one could tell they were made with whole grains!
If you want to know more about milling your own flour, check out my post a Beginner’s Guide to Milling Flour at Home.
Why you’ll love this whole wheat chocolate chip cookie recipe
- No chill needed (see my test results below!)
- Classic chewy texture
- Doesn’t taste like whole wheat at all
- Quick and easy recipe
- Makes dozens of 1-inch cookies
- Can be made with several types of wheat
- Slight nutty flavor from the wheat berries
Equipment
- Grain mill (I have a Harvest mill from Nutrimill, which works great for this recipe)*
- Stand mixer with paddle attachment or large mixing bowl with hand mixer
- Sheet pans
- Parchment paper or silicone mats
- Cookie scoop
- Wire rack
*Technically, you are not supposed to double mill with many electric grain mills. I don’t do it often – only for cookies – and have had no problems, but each mill is different.
Learn more about the Best Supplies for Home Milling here.
Ingredients
- Soft white wheat flour – I used fresh flour from soft white wheat berries I got from Azure Standard. The trick is to process it until it is super soft and fluffy. My first batch was gritty and overly chewy, and I realized it was because the flour wasn’t fine enough. You can also sift the flour if you want to remove any extra bran or anything.
- Unsalted butter – Fully softened to room temperature. If you use salted butter, reduce the salt in the recipe.
- Brown sugar & white sugar – The combination of both sugars gets the perfect bite on the edges and chewy texture on the inside.
- Vanilla extract – I used my homemade vanilla extract, which has a really rich vanilla flavor.
- Eggs
- Baking soda & baking powder – For just enough rise
- Kosher salt
- Dark chocolate chips – Either dark or semi-sweet chocolate chips work well. You can also use white chocolate or milk chocolate, but I prefer a little bitterness to offset the sweetness.
How to Make Chocolate Chip Cookies with Fresh Milled Flour
- Preheat oven to 350 F and line sheet pans with parchment paper.
- Mill the flour, running it through the grain mill again, if needed, to make it soft and fluffy. (Keep in mind that not all mills should be used for this and you may void the warranty.)
- Add the butter and sugars to the bowl of the stand mixer and cream over medium speed for 2-3 minutes or until light and fluffy.
- Add the vanilla extract and eggs and whisk until combined.
- Add the baking powder, baking soda, salt, and flour gradually, continuing to stir until the cookie dough comes together.
- Stir in the chocolate chips until incorporated. Be careful not to overmix.
- Scoop even-sized portions of cookie dough onto each cookie sheet. I used a small cookie scoop.
- Bake for 10-12 minutes, removing the cookies from the oven when the edges just begin to turn golden brown.
- Allow the cookies to continue cooling on the sheet pans for 2-3 minutes then transfer to a wire rack.
- Enjoy warm or cool to room temperature then store in an airtight container for 2-3 days.
Storing Suggestions
Cookies have the best flavor and texture at room temperature, but they go stale quickly. It’s best to store at room temperature for about 2 days or refrigerate for up to a week. I often freeze extra cookies in a freezer bag and pull a few out at a time for a little snack.
You can also scoop and freeze cookie dough balls on sheet pans and freeze solid. Transfer to a freezer-safe container and any time you want to bake some cookies, either thaw in the fridge and bake like normal or bake from frozen (extend the cooking time and additional few minutes).
How to Use
These cookies genuinely taste just like regular chocolate chip cookies! They’re great in any preparation, ideally served with a cold glass of milk or crumbled over ice cream. They also make great ice cream sandwiches!
Tips & Variations
To chill or not to chill? I baked several versions of this recipe to see if I really needed to chill the dough. Here are the results:
- No chill – Cookies were slightly flatter than later batches with a really nice chewiness.
- Chilled for 15 minutes – Cookies were almost identical to the no-chill batch, but were slightly softer.
- Chilled for 30 minutes – Cookies were a little taller and puffier.
Based on these results, it’s clear to me that there really isn’t a huge difference between chilling or not. If you prefer a chewier cookie, don’t chill. If you want a slightly softer, taller cookie, do chill.
- Technically, you can make this recipe with regular white flour if you want! It actually works well with both.
- If you want an even softer, chewier cookie, add 1-2 TBS cornstarch to the cookie dough.
- I like to use chocolate chips made with less sugar (they sell some at Costco), but you can use any type you prefer.
FAQs
The good news is that cookies do not require a high protein or gluten content, so soft wheat berries are perfect. But you can really use almost any type of fresh milled grain. I’ve tested this recipe with hard white wheat berries and soft white wheat berries, and they both turned out well. I do recommend sticking to the white wheat family, as it has a mild flavor that lets the flavor of the brown sugar and chocolate chips stand out.
When I first tested this recipe, I processed my wheat berries just once on a fine setting. I realized that all of the bran was causing the dough to seem like it didn’t have enough flour, and they were really firm and chewy, almost like florentines.
I decided to process the whole grain flour again until it was really soft and fluffy with no visible bran. This made a huge difference! The flour works just like all purpose flour in this recipe and helps the cookies hold together really well.
Related Recipes
If you made this recipe, please leave a comment or ask a question below! I’d love to hear what you think or troubleshoot any issues.
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Chewy Chocolate Chip Cookies with Fresh Milled Flour
Equipment
- Half sheet pans
- Parchment paper or silicone mats
- Cookie scoop
- Wire rack
Ingredients
- 1 cup unsalted butter, softened to room temperature
- 1 cup brown sugar
- 1 cup white sugar
- 2 tsp vanilla extract
- 2 eggs
- 3 cups soft white wheat flour, freshly milled; process twice if needed until soft and fluffy
- 1 tsp baking soda
- 1 tsp baking powder
- 1 1/2 tsp kosher salt, if using table salt, use 1 tsp or less
- 1 1/2 cups dark chocolate chips
Instructions
- Preheat oven to 350 F and line sheet pans with parchment paper.
- Mill the flour, running it through the grain mill again, if needed, to make it soft and fluffy.
- Add the butter and sugars to the bowl of the stand mixer and cream over medium speed for 2-3 minutes or until light and fluffy.1 cup unsalted butter, 1 cup brown sugar, 1 cup white sugar
- Add the vanilla extract and eggs and whisk until combined.2 tsp vanilla extract, 2 eggs
- Add the baking powder, baking soda, salt, and flour gradually, continuing to stir until the cookie dough comes together.1 tsp baking soda, 1 tsp baking powder, 1 1/2 tsp kosher salt, 3 cups soft white wheat flour
- Stir in the chocolate chips until incorporated. Be careful not to overmix.1 1/2 cups dark chocolate chips
- Scoop even-sized portions of cookie dough onto each cookie sheet. I used a small cookie scoop.
- Bake for 10-12 minutes, removing the cookies from the oven when the edges just begin to turn golden brown.
- Allow the cookies to continue cooling on the sheet pans for 2-3 minutes then transfer to a wire rack.
- Enjoy warm or cool to room temperature then store in an airtight container for 2-3 days.
Notes
- No chill – Cookies were slightly flatter than later batches with a really nice chewiness.
- Chilled for 15 minutes – Cookies were almost identical to the no-chill batch, but were slightly softer.
- Chilled for 30 minutes – Cookies were a little taller and puffier.
Did you try this recipe?
Post a photo and tag @milkglasshome!Pin this recipe for later!
Hi, it says eggs in the directions, but there aren’t any eggs listed in the ingredients list for the recipe section.
So sorry about that! There are 2 eggs in the cookie dough. I just adjusted the recipe card. Thanks for letting me know!
Delicious
My family loves these. They disappear so fast and no one can tell they are whole wheat.
Yay, that’s exactly how we feel about them, too! They taste just like regular chocolate chip cookies to us. Thanks for sharing! 🙂
You might add a note that only if you have a stone mill to mill twice especially for beginners. Not all mills can double mill for instance an impact mill like the Nutrimill Classic. But to mill on the finest setting for impact or double mill for stone mills. Just a suggestion. But they look yummy.
I just made these and they are very tasty! But since I have been using fresh milled flour my cookies have come out flat! Is there something I am potentially doing to cause this or do you have any suggestions on how to fix this? Thanks
Hi, Cheryl! Thanks for your question. I’ve been thinking about it for a couple of days and suspect the issues come from 1) the flour being too coarse, 2) dough temperature, or 3) out-of-date leavening agent or ingredient substitution.
I suspect it’s probably the first one. When I first started making cookies with fresh flour, I wasn’t milling the flour fine enough and the cookies were flat and really chewy. Good, but VERY flat! Once I started double-milling (not recommended for all mills; I’m breaking the rules with mine), it totally changed and acted much more like regular flour.
If your flour is really fine, then you may want to try chilling the dough first. Although I didn’t need to in my recipe testing, it may help in this situation.
Finally, you may want to check that your baking soda and baking powder are both active and effective. If you made any ingredient substitutions (like margarine for butter or something), I’d skip those.
Ultimately, I’d bet it is the fineness of the flour, but I hope these ideas help!
I loved the chewyness of it ❤️❤️ its really healthy too!!!
Some of the best cookies I’ve had! Easy recipe to follow and a crowd favorite.
This recipe was fantastic ! I didn’t have to double mill my flour and I just added a splash of whole milk.
Can I freeze some of this? I don’t need 5 dozen at one time but would love to scoop them and freeze them if I can.
Absolutely! You can even bake from frozen, but may need to add a couple minutes to the baking time.