Fresh Milled Flour Chocolate Chip Cookies
These Fresh Milled Flour Chocolate Chip Cookies are thick, soft and chewy with plenty of chocolate in every bite! They have the classic chocolate chip cookie texture and flavor you love but made with whole grains!
Love to bake Fresh Milled Flour Recipes? Check out my Fudgy Spelt Brownies, Snickerdoodles, or Whole Wheat Biscuits.

SAVE THIS RECIPE FOR LATER!
I recently went back and tweaked my original recipe, and these turned out even better! A blend of freshly milled soft white wheat and hard white wheat, along with a little cornstarch and a short chill, gives the cookies the perfect texture while still keeping them soft and chewy.
My goal with Fresh milled flour desserts is always to make something my family would love whether they knew it was whole wheat or not!
What you’ll love about about these Whole Wheat Cookies:
Recipe Ingredients
You’ll need the following ingredients to make these amazing Whole Wheat Chocolate Chocolate Chip Cookies:
- Butter
- White Sugar
- Brown Sugar
- Eggs
- Vanilla Extract
- Fresh Milled Soft White Wheat Flour
- Fresh Milled Hard White Wheat Flour
- Cornstarch
- Baking soda
- Salt
- Chocolate Chips

INGREDIENT NOTES:
- Freshly Milled Soft White Wheat Flour: Soft white wheat has a mild flavor and works especially well in cookies and other baked goods where you want a softer texture.
- Freshly Milled Hard White Wheat Flour: Adding hard white wheat gives these cookies a little more structure. I found out that using a combination of soft white and hard white wheat gave me a better texture than using soft white alone.
- Cornstarch: Just a couple teaspoons helps keep the cookies soft while also giving the dough a little more structure.
- Butter: Make sure your butter is softened, but not overly warm or melted. Butter that is too warm can cause the cookies to spread too much.
How to make Fresh Milled Flour Chocolate Chip Cookies
STEP 1: Cream the softened butter, white sugar, and brown sugar until creamy. Add the eggs and vanilla; mix until combined
STEP 2: In a separate bowl, whisk together both flours, cornstarch, baking soda, and salt.
STEP 3: Slowly add the dry ingredients to the wet ingredients and mix just until combined. Fold in the chocolate chips.
STEP 4: Line a baking sheet with parchment paper. Scoop the cookie dough onto the sheet and place in the refrigerator for at least 30 minutes.
STEP 5: Preheat the oven to 375 degrees F while the dough chills.
STEP 6: Bake for 8-10 minutes, until the edges are lightly golden and the centers still look soft. Do not overbake.
STEP 7: Allow the cookies to cool on the baking sheet for 5 minutes before transferring them to a wire rack to cool completely. Top the cookies with additional chocolate chips and sprinkle with flaky sea salt if desired.



PRO TIP:
Don’t wait for the centers of the cookies to look completely done before taking them out of the oven. They will continue to set as they cool on the baking sheet. This keeps the centers soft and chewy instead of dry.
Storage and Reheating
Storage: Store cooled cookies in an airtight container at room temperature for up to 4 days.
Reheating: To enjoy warm cookies, microwave them for 10-15 seconds.
Freezer: Place completely cooled cookies in a freezer safe container, or Ziploc bag and freeze for up to 3 months. Thaw at room temp before serving.
Freeze the Dough: Scoop the cookie dough into portions and freeze on a baking sheet until firm. Transfer the frozen dough balls to a freezer bag and keep frozen until you’re ready to bake them. Bake from frozen, they usually need an extra couple minutes.

Additions & Substitutions
ADDITIONS:
- Chocolate Chunks: Replace some or all of the chocolate chips with semi-sweet chocolate chunks for larger pockets of melted chocolate. My original recipe had chunks! We love them, I just always have chocolate chips on hand!
- Flaky Sea Salt: Sprinkle a little flaky sea salt over the cookies while they’re still warm. The salty-sweet combination is SO good!
SUBSTITUTIONS:
- Flour: You can use all soft white wheat, or all hard white wheat instead of the blend.
- Different Chocolate Chips: Milk chocolate, dark chocolate, or a combo of chocolate will all work!
FAQs about these Fresh Milled Flour Chocolate Chip Cookies:
What is the best wheat for freshly milled flour chocolate chip cookies?
I love a combination of soft white and hard white wheat for this recipe. Soft white wheat keeps the cookies tender, while hard white wheat gives them a little more structure and helps keep them from spreading too thin.
Why do you chill fresh milled flour cookie dough?
Chilling the dough gives the fresh milled flour time to absorb some of the moisture and helps firm up the dough, which keeps the cookies from spreading too much.
Why are my whole wheat chocolate chip cookies spreading too much?
Butter that is too warm, skipping the chill time, or not using enough flour can all cause the cookies to spread more. Chill this dough for the full 30 minutes before baking and make sure the butter is softened, not melted.

What Can I Serve with these Chocolate Chip Cookies made with Fresh Milled Flour?
Serve these cookies with a cold glass of milk, pack them in lunchboxes, or keep a batch in the freezer when you want something sweet and whole grains!
Made this recipe? I’d love to see it! Tag me on IG or FB @littlechefwithin or share a photo in my Facebook group, Fresh Milled Flour Happiness. I love seeing what you’re baking!

Whole Wheat Chocolate Chip Cookies (Fresh Milled Flour)
Equipment
Ingredients
- 1 cup salted butter (226g) softened
- 3/4 cup granulated sugar (150g)
- 3/4 cup brown sugar (160g) packed
- 2 large eggs
- 2 teaspoons vanilla extract (10g)
- 1 1/2 cups freshly milled soft white wheat flour (168g)
- 1 3/4 cups freshly milled hard white wheat flour (196g)
- 1 teaspoon baking soda (5g)
- 2 teaspoons cornstarch (6g)
- 1/2 teaspoon salt (3g)
- 2 cups semi-sweet chocolate chips (340g)
Instructions
- In a large mixing bowl, beat the softened butter, granulated sugar, and brown sugar until light and creamy. 1 cup salted butter (226g),3/4 cup granulated sugar (150g),3/4 cup brown sugar (160g).
- Add the eggs and vanilla extract and mix until well combined. 2 large eggs,2 teaspoons vanilla extract (10g).
- In a separate bowl, whisk together the freshly milled soft white wheat flour, hard white wheat flour, cornstarch, baking soda, and salt. 1 1/2 cups freshly milled soft white wheat flour (168g),1 3/4 cups freshly milled hard white wheat flour (196g),1 teaspoon baking soda (5g),2 teaspoons cornstarch (6g),1/2 teaspoon salt (3g).
- Gradually add the dry ingredients to the wet ingredients and mix just until combined Fold in the chocolate chips.2 cups semi-sweet chocolate chips (340g).
- Line a baking sheet with parchment paper. Scoop the cookie dough onto the prepared baking sheet, spacing the cookies about 2 inches apart.
- Place the entire baking sheet(s) in the refrigerator and chill the cookie dough balls for at least 30 minutes.
- Preheat the oven to 375°F while the dough chills.
- Remove the baking sheet from the fridge and place it directly into the preheated oven. Bake for 8-10 minutes until the edges are lightly golden and the centers still look soft.
Notes
Nutrition
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Excellent recipe! Easy, quick and delicious
These look amazing! I’m definitely going to make these!