These fresh milled chocolate chip cookies are about to be your new favorite cookie recipe. Made with freshly milled soft white wheat flour, this is a sweet treat that is not only delicious, but one that you can feel good about.

Cookie with a bite taken out of it.

Throughout the years, I have started baking more and more with freshly-milled flour. From whole wheat biscuits and freshly milled sourdough bread to sweet treats like this chocolate chip cookie recipe. We have been enjoying nutrient packed baked goods quite often.

Milling your own flour makes for the best homemade chocolate chip cookies. Not only do you get delicious cookies that make great ice cream sandwiches or are perfect for dipping in a cold glass of milk, but you also get all the nutritional benefits of whole grain flour. 

With their irresistible chewy texture and sweet chocolate morsels, these cookies are about to become a new staple in your collection of healthy recipes. Enjoy one fresh from the oven with a glass of milk as an afternoon snack, or as a much earned way to end the day after a hearty dinner like creamy chicken and wild rice soup or burger bowls with special sauce

Why You’ll Love This Recipe

Nutritious – While cookies are a sweet treat, when you bake with whole wheat, especially freshly milled whole wheat, you end up enjoying more of the nutritional benefits not found in all purpose flour.

Delicious – These whole-wheat chocolate chip cookies have a unique and delicious depth of flavor and nutty taste thanks to freshly milled grains.

Simple – Made with simple ingredients and a breeze to whip up, these sweet morsels are all you could ever want out of a dessert!

Ingredients

Ingredients for fresh milled chocolate chip cookies on a counter top.

Freshly milled soft white flour – You can sub regular whole wheat flour, but there may be differences in moisture and texture when made with another flour. Want to learn more about baking with freshly milled grains? Check out my Freshly Milled Grains online mini-course here.

Chocolate chips – Milk chocolate chips, dark chocolate chips, or semi-sweet chocolate chips can be used based on your preference. If you are a white chocolate fan, add in some white chocolate chips or chunks in the mix, too. 

A full ingredient list with exact amounts can be found in the recipe card below.

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Tools You May Need

How to Make Fresh Milled Chocolate Chip Cookies

Dry ingredients in a bowl with a whisk.

Step 1: Preheat oven to 375 degrees Fahrenheit. Line baking sheets with parchment paper.

In a medium mixing bowl, whisk the flour, baking soda, baking powder, and salt until well combined. Set aside.

Butter and sugar creamed together in a stand mixer.

Step 2: In a bowl of a stand mixer or in a large bowl with an electric mixer, cream the butter with both sugars until smooth and creamy. Add the eggs and vanilla, then beat for about a minute until the mixture looks lighter and a little fluffy.

Dry and wet ingredients mixed together.

Step 3: Mix in the dry ingredients with the wet ingredients and mix.

Chocolate chips added in a dough.

Step 4: Stir in the chocolate chips. Careful not to over mix.

Dough balls on a cookie sheet.

Step 5: Scoop mounds of dough, about 2–3 tablespoons of dough per cookie, roll into balls, and place them on the prepared pans with space between each one.

Cookies on a cooling rack.

Step 6: Bake cookies for 8–10 minutes, pulling them out when the edges are barely starting to turn golden brown. Let the cookies rest on the baking sheet for 5 minutes, then move them to a wire rack.

Stacked chocolate chip cookies.

Tips 

  • Sub in dark chocolate chunks for chocolate chips and top with a sprinkle of sea salt. This makes for a truly delicious cookie. 
  • Use a cookie scoop to efficiently scoop the dough and end up with consistent cookie dough balls. 
  • Be sure to not over mix the dough to end up with softer cookies.
  • To avoid flat cookies, chill the dough before baking. 

Recipe FAQs

What types of wheat berries are recommended for fresh milling in chocolate chip cookies?

I recommend using a soft white wheat berries for this recipe. 

What is the healthiest flour to eat?

Freshly milled flour is the most nutritious flour due to the fact that it retains all the nutrients found in wheat. We also love to bake with ancient grains such as einkorn, spelt, and rye flour. (You can make chocolate chip cookies with einkorn flour, too!)

How to store whole wheat cookies?

Store these cookies in an airtight container at room temperature for about a week. You can also freeze the cookies (or the dough!) for up to two to three months.

Chocolate Chip Cookies with Fresh Milled Flour

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These fresh milled chocolate chip cookies are about to be your new favorite cookie recipe. Made with freshly milled soft white wheat flour, this is a sweet treat that is not only delicious, but one that you can feel good about!
Prep: 20 minutes
Cook: 10 minutes
Total: 30 minutes
Servings: 36 Cookies
Cookies laid out on the counter.
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Equipment

Ingredients

  • 1 cup butter, softened, 227 grams
  • 1 cup granulated sugar, 192 grams
  • 1 cup light brown sugar, packed, 200 grams
  • 2 teaspoons pure vanilla extract, 10 grams
  • 2 large eggs
  • 3 cups fresh milled soft white flour, 390 grams
  • 1 teaspoon baking soda
  • ½ teaspoon baking powder
  • 1 teaspoon sea salt, 5 grams
  • 2 cups chocolate chips

Instructions 

  • Preheat oven to 375 degrees Fahrenheit. Line baking sheets with parchment paper.
  • In a medium mixing bowl, whisk the flour, baking soda, baking powder, and salt until well combined. Set aside.
  • In a bowl of a stand mixer or in a large bowl with an electric mixer, cream the butter with both sugars until smooth and creamy. Add the eggs and vanilla, then beat for about a minute until the mixture looks lighter and a little fluffy.
  • Mix in the dry ingredients with the wet ingredients and mix. Stir in the chocolate chips.
  • Scoop mounds of dough, about 2–3 tablespoons of dough per cookie, roll into balls, and place them on the prepared pans with space between each one.

Notes

  • Sub in dark chocolate chunks for chocolate chips and top with a sprinkle of sea salt. The large chunks of chocolate and sea salt addition can really elevate a basic cookie recipe. 
  • Use a cookie scoop to efficiently scoop the dough and end up with consistent cookie dough balls. 
  • Be sure to not overmix the dough to end up with softer cookies.
  • Experiment with chilling the dough in the fridge for thicker cookies.

Nutrition

Serving: 1cookie | Calories: 182kcal | Carbohydrates: 26g | Protein: 1g | Fat: 8g | Saturated Fat: 5g | Polyunsaturated Fat: 0.3g | Monounsaturated Fat: 1g | Trans Fat: 0.2g | Cholesterol: 23mg | Sodium: 147mg | Potassium: 53mg | Fiber: 0.3g | Sugar: 17g | Vitamin A: 171IU | Calcium: 20mg | Iron: 1mg

Nutrition information is automatically calculated, so should only be used as an approximation.

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