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Home » Cookies » Chocolate Chip Cookies with Fresh Milled Flour

Chocolate Chip Cookies with Fresh Milled Flour

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May 1, 2025 by Angelica 4 Comments

I confess – Chocolate Chip Cookies are my favorite! Well, along with oatmeal coconut cookies, ice cream, and chocolate cake. Those are all my favorite too! Seriously though, chocolate chip cookies are many people’s favorite cookie for a good reason: they are simple and delicious! This particular recipe makes a few healthy tweaks to the classic cookie.

fresh milled chocolate chip cookies on cooling tray seen from overhead
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Since I love chocolate chip cookies, it was a must to develop a recipe that works well with fresh milled flour. Even though cookies are a treat, I want these cookies to be as healthy as possible – and still delicious! These cookies are made with 100% unsifted fresh milled flour and reduced sugar, and the result is thick, soft and chewy cookies that are every bit as crave-worthy as ones made with traditional ingredients.

Want the classic back-of-the-bag version? See my tested Toll House cookies with fresh milled flour. This post details what I learned, what I changed and why. And for a little variety, try my Fresh Milled Peanut Butter Cookies as well. So easy and so good. You can’t have too many cookies, right?

Chocolate Chip Cookies with Fresh Milled Flour

No, these cookies are not “health food” but they do fit much better into my goals of avoiding refined flour and sugar. If you have similar goals, read on.

chocolate chip cookies made with freshly ground flour on cooling tray seen from the side

About This Recipe:

  • My first goal with this recipe was simply to use fresh milled flour instead of all-purpose. I like to use soft grains for these, such as soft white wheat or a combination of soft white and einkorn.
  • My second goal was to reduce overall sugar content and use less refined sweeteners as much as possible.
  • Finally, I wanted this recipe to be simple! No browned butter, no special chocolate, no fancy ingredients for this one. Just a simple, straightforward chocolate chip cookie that I can customize with add-ins as desired.

Ingredients

Let’s run through the ingredients:

Butter – I use regular, salted butter. I know the preference for many bakers is to use unsalted butter so that salt can be controlled more precisely. For me, it’s not worth the hassle of keeping two different types of butter in my fridge at all times. Basically, use what you have on hand, as long as it’s real butter.

Flour – I used soft white wheat berries for the batch pictured. You can definitely mill other soft grains, such as einkorn, spelt or barley, if you happen to have those on hand. I’ve been doing a mix of soft white and einkorn lately and I really like that combo as well.

You can also include some hard wheat in these cookies. Honestly, cookies are very flexible. Just about any combination of grains will work. I like to stick with soft grains but others use all or part hard grains in their cookies. I actually haven’t done that yet but it’s worth trying. Just keep in mind you may need to adjust the amount of flour a little bit to get the desired texture. The goal is to get a thick, somewhat stiff dough. I always recommend doing a test cookie or two before baking a full tray. That way you can still adjust if you find the results are not what you want.

New to fresh milled flour? Check out my getting started guide for everything you need to know.

If you are using store-bought flour, I would use a white whole wheat flour. You might start with a little less flour and add more if needed to get the right texture.

Brown Sugar/Sucanat – you can absolutely use brown sugar if you prefer. I like to use sucanat because it is less processed and well, it seems like a cleaner, healthier sweetener to use. Does that mean I don’t ever use brown sugar? No, I still use it in some situations. For cookies, I have found sucanat to work just fine and I like the flavor so I’ve been using that a lot. It is not moist like brown sugar but does have that rich molasses flavor.

chocolate chip cookies with walnuts made with whole grain fresh milled flour on white plate seen from overhead

Sugar: You can absolutely use regular white sugar for the most traditional taste and texture. These are cookies, after all!

However, if you want to cut down on sugar, I’ve found that a combination of erythritol and regular sugar works beautifully. I currently use 1/2 cup erythritol and 1/4 cup cane sugar, and I love the result. You get that classic cookie texture with crispy edges while still reducing the overall sugar content.

Of course, you can also experiment with other alternative granulated sweeteners like allulose, monk fruit, or xylitol. Just keep in mind that different sweeteners will affect the spread, taste, and texture of your cookies.

I have also often made them with all allulose (along with the sucanat), which results in a softer cookie without those crispy edges. I still love those as well and I am happy there are so many great options to experiment with!

Eggs: I used regular store-bought large eggs. I haven’t tried any egg replacement methods in this recipe but it would likely work fine.

Chocolate chips: You can use any kind of chips you like. I used regular semi-sweet chips for the cookies pictured. Sugar-free chips would work beautifully as well, or a mix of chips. My favorite combo is a mix of sugar-free, dark chocolate and semi-sweet chips.

Of course, chocolate chunks would work great as well, if you want to go that route.

Nuts: I used chopped walnuts here but pecans would also be great. Or you can skip the nuts altogether if you prefer.

Salt: I typically use Himalayan pink salt or a fine sea salt such as Redmond Real Salt in my baking. These are coarser than regular table salt. If you’re using fine table salt, reduce the amount to 3/4 teaspoon since table salt is more concentrated and packs more saltiness per teaspoon.

Other ingredients: You will also need basic pantry ingredients including vanilla and baking soda.

Instructions

Mixing bowl with dry ingredients for Chocolate Chip Cookies with fresh milled flour
Sift dry ingredients.
Mixing bowl with butter, sucanat and allulose for Chocolate Chip Cookies with fresh milled flour
Cream butter and sugars.
Mixing bowl with creamed butter and sugar for Chocolate Chip cookies with fresh milled flour dough, with vanilla and one egg added
Add vanilla and eggs, one at a time.
Adding chocolate chips and nuts to Chocolate Chip cookies with fresh milled flour dough
Add mix-ins
Mixing bowl with dry ingredients added to Chocolate Chip cookies with fresh milled flour dough.
Add dry ingredients and mix.
Finished dough for Chocolate Chip Cookies with fresh milled flour
Finished dough
Chocolate Chip Cookies with fresh milled flour dough balls on baking sheet
Scoop onto parchment-lined cookie sheet. I like to leave plenty of room between them.

This is your typical drop cookie recipe, which means it comes together pretty quickly.

  1. Prepare your dry ingredients and set aside.
  2. Cream the room-temperature butter with the sugars until fluffy.
  3. Add vanilla and then eggs, one at a time, and mix until well combined.
  4. Add flour mixture in three parts to creamed butter mixture. Mix just enough to combine each time.
  5. Add your mix-ins and mix briefly just to distribute.
  6. Preheat the oven to 350°F. Allow the dough to rest for 10-15 minutes while the oven comes to temperature.
  7. Scoop portions using large cookie scoop and roll into balls. Place on baking trays and bake 11-13 minutes, or until lightly brown at the edges.
  8. Allow to cool on baking trays for 10-15 minutes before moving to cooling trays.

NOTE: When ready to bake, I always recommend baking one or two cookies first. This way you can see how much they spread. If they spread too much, you can try adding a little more flour, chilling the dough for a while or just let the dough sit longer for the flour to absorb moisture. If they don’t spread at all and stay in a mound, you might try flattening them slightly so they bake more evenly. In my testing, these spread just the right amount but your batch may be slightly different.

a stack of chocolate chip cookies made with fresh milled flour with top cookie showing inside texture and melty chocolate

Common Questions

Should I sift my fresh milled flour?

I didn’t sift this flour at all; I don’t find it necessary for this recipe either for aeration or for removing some of the bran. I personally love cookies with unsifted flour so I have not experimented with sifting fresh milled flour for cookies at this point.

Can I substitute store-bought flour?

Yes, you can substitute store-bought white whole wheat flour. I’d recommend using a white whole wheat variety like Wheat Montana Prairie Gold 100% Whole Wheat Flour. I think you would want to decrease the amount of flour a bit since store-bought flour tends to be drier and more finely milled than fresh milled.

Can I freeze the cookies?

Yes, you can absolutely freeze these! I like to freeze dough balls on a cookie sheet. Once fully frozen, I put them in a bag with date and baking instructions. Just add a minute or two to baking times since the dough starts out frozen.

You could also fully bake the cookies and then freeze. Once frozen, wrap each cookie individually and place in a storage bag.

Other Recipes You Might Enjoy:

Oatmeal Raisin Cookies

Oatmeal Coconut Cookies

Soft Pumpkin Cookies

Did you try this recipe? Leave a ⭐⭐⭐⭐⭐ rating below and save it on Pinterest for later!

overhead view of fresh milled chocolate chip cookies on cooling tray

Chocolate Chip Cookies with Fresh Milled Flour

Angelica
Soft, chewy Chocolate Chip Cookies made with fresh milled whole wheat flour. These have all the classic flavor with the wholesome goodness of whole grains.
4.50 from 2 votes
Print Recipe Pin Recipe
Prep Time 15 minutes mins
Cook Time 11 minutes mins
Resting Time 15 minutes mins
Total Time 41 minutes mins
Course Dessert, Snack
Cuisine American
Servings 18 large cookies

Ingredients
  

  • 2 1/4 cups (270g) fresh milled flour *see notes
  • 3/4 cup (150g) sugar or alternative granulated sweetener
  • 1/4 cup brown sugar or sucanat
  • 1/2 cup (1 stick) butter room temperature
  • 2 eggs room temperature
  • 2 tsp vanilla extract
  • 1 tsp salt (I use Himalayan pink salt) If using table salt, decrease to 3/4 teaspoon
  • 1 tsp baking soda
  • 1 cup chocolate chips
  • 1/2 cup chopped walnuts

Instructions
 

  • Line baking trays with parchment paper. I like to lightly spray the tray and then smooth down the parchment paper so it won't move around.
  • In medium bowl, whisk flour, baking soda and salt. Set aside.
  • Cream butter and sugar until light and fluffy.
  • Add vanilla and then eggs, one at a time. Mix until well combined.
  • Add flour mixture in three parts, mixing just until smooth each time.
  • Add chocolate chips and walnuts and mix just until incorporated.
  • Preheat oven to 350°F. Allow dough to rest until oven comes to temperature, about 10-15 minutes.
  • Scoop onto parchment-lined baking trays using large (4 tablespoon) cookie scoop. Roll into balls. Place cookie balls at least 2 inches apart on baking trays. I like to cook no more than 8 cookies per tray to allow plenty of room.
  • I typically bake only one tray at a time in middle rack. If baking two trays, it helps to rotate the trays about halfway through baking.
  • Bake for 11-13 minutes until lightly brown at the edges. The center should look a bit wet.
  • Allow to cool on baking trays for 10-15 minutes and then remove to cooling trays.
  • NOTE: I always recommend baking 1 or 2 cookies to test how much they spread first. You might find you need to flatten slightly if not spreading enough. Alternatively, if they spread too much, allow dough to rest longer or chill dough balls for an hour or two before baking.

Notes

*I slightly increased the flour content to 270g (from 240g) to yield thicker cookies. If you found the lesser amount of flour to work best for you, keep doing that.

Common Questions

Should I sift my fresh milled flour?
I didn’t sift this flour at all; I don’t find it necessary for this recipe either for aeration or for removing some of the bran. I personally love cookies with unsifted flour so I have not experimented with sifting fresh milled flour for cookies at this point.
Can I substitute store-bought flour?
Yes, you can substitute store-bought white whole wheat flour. I’d recommend using a white whole wheat variety like Wheat Montana Prairie Gold 100% Whole Wheat Flour. I think you would want to decrease the amount of flour a bit since store-bought flour tends to be drier and more finely milled than fresh milled.
Can I freeze the cookies?
Yes, you can absolutely freeze these! I like to freeze dough balls on a cookie sheet. Once fully frozen, I put them in a bag with date and baking instructions. Just add a minute or two to baking times since the dough starts out frozen.
You could also fully bake the cookies and then freeze. Once frozen, wrap each cookie individually and place in a storage bag.
Keyword chocolate chip, cookies, fresh milled flour, easy
Tried this recipe?Let us know how it was!

Pin for later!

pin image with fresh milled chocolate chip cookie against a glass of milk

Filed Under: Cookies Tagged With: easy, fresh milled flour, reduced sugar

Previous Post: « Fresh Milled Oatmeal Coconut Cookies
Next Post: Fresh Milled Flour Granny Cake »

Reader Interactions

Comments

  1. Jasmine Martinez says

    August 5, 2025 at 2:01 pm

    5 stars
    These cookies are delicious! They taste just like Chips Ahoy chewy cookies and you wouldn’t even be able to tell they were healthy. My kids loved them too!

    Reply
    • Angelica Montero says

      August 5, 2025 at 2:06 pm

      Thank you Jassy! So happy you and the kids loved them!

      Reply
  2. m98 ทางเข้า says

    April 19, 2026 at 8:47 pm

    4 stars
    Wow, awesome blog layout! How long have you been blogging for?
    you made blogging look easy. The overall look of your web site is
    wonderful, let alone the content!

    Reply
    • Angelica says

      April 20, 2026 at 8:39 am

      Thank you, I appreciate that so much. I started blogging just about a year ago and I am enjoying it tremendously. Hopefully, that shows in my blog and my content. Thanks again for visiting and for your support!

      Reply
4.50 from 2 votes

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Hi, I’m Angelica. I share flexible baking recipes with whole grains, less sugar, and (mostly!) healthy ingredients – whether that’s fresh milled flour or whatever’s on hand. My goal? To keep baking flexible so it fits your life, just like it fits mine. READ MORE.

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