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Whole Wheat Chocolate Chip Cookies

These Whole Wheat Chocolate Chip Cookies are made with freshly milled soft white wheat flour, giving them a rich whole grain flavor while still staying soft and chewy just like classic chocolate chip cookies.

Are you looking for more Whole Wheat Recipes? Try our Banana Cake, Whole Wheat Pancakes, and Cinnamon Rolls with Fresh Milled Flour.

If you’re new to baking with freshly milled flour, you may want to start with my Freshly Milled Flour 101 post. It walks through what to expect and explains why freshly milled flour behaves differently than store-bought flour.

Homemade chocolate chip cookies with a glass of milk and milk bottles.

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These Whole Wheat Chocolate Chip Cookies are a wholesome twist on a classic, made with freshly milled soft white wheat flour for a rich, nutty flavor and soft texture. They’re packed with plenty of chocolate chips and still have that same delicious chewy bite everyone loves.

Soft white wheat is ideal for cookies because it has a lower protein content, which helps create a softer, more tender texture.

What you’ll love about about these Whole Wheat Cookies:


  • WHOLESOME – Made with whole wheat flour, these cookies are a healthier version of your favorite treat.
  • SOFT & CHEWY – Perfectly soft in the center with just the right amount of chew.
  • LOADED WITH CHOCOLATE – These cookies are packed with both semi-sweet chocolate chips and chunks for double the chocolatey goodness.

Baking cookies with whole grain flour adds a rich, nutty flavor while still giving you the classic taste of homemade chocolate chip cookies. The next time you’re craving something sweet, these cookies are an easy way to enjoy a treat with a little extra whole grain goodness.

Recipe Ingredients

You’ll need the following ingredients to make these amazing Whole Wheat Chocolate Chocolate Chip Cookies:

  • Salted butter
  • Granulated sugar
  • Light brown sugar
  • Large eggs
  • Vanilla extract- I love to use pure vanilla extract.
  • Freshly Milled Soft White Wheat Flour
  • Baking soda
  • Salt
  • Semi-sweet chocolate chips
  • Semi-sweet chocolate chunks
Chocolate chips, brown sugar, butter, eggs, vanilla extract, whole wheat flour, white sugar, baking soda, salt, and chocolate chunks on a textured surface.

INGREDIENT NOTES:

  • Fresh Milled Flour: Soft white wheat creates a lighter, more tender cookie than hard wheat varieties. Freshly milled flour absorbs moisture differently than store-bought flour, so the dough may need a short rest before baking.
  • Chocolate chunks: Chocolate chunks add larger bites of chocolate and give the cookies a bakery-style look and texture. You can totally use all chocolate chips or all chocolate chunks instead.

HOW TO MAKE WHOLE WHEAT CHOCOLATE CHIP COOKIES STEP-BY-STEP:

Check out the quick visual guides below. For full instructions and ingredients, see the printable recipe card at the end.

STEP 1: Preheat the oven to 375 F and line two baking sheets with parchment paper.

STEP 2:  In the bowl of a stand mixer fitted with the paddle attachment, cream together the softened butter, granulated sugar, and brown sugar on medium speed until the mixture is light and fluffy.

STEP 3: Beat in the eggs, one at a time, and then stir in the vanilla extract.

STEP 4: In a separate bowl, whisk together the freshly milled flour, baking soda, and salt. Gradually add this dry mixture to the wet ingredients, mixing until just combined.

STEP 5: Fold in the semi-sweet chocolate chips and chocolate chunks.

STEP 6: Using a cookie scoop, drop spoonfuls of dough onto the prepared baking sheet, spacing them about 2 inches apart. Bake for 10-11 minutes, or until the edges are lightly golden, and the centers remain soft.

STEP 7: Allow the cookies to cool on the baking sheet for a few minutes before transferring them to a wire rack to cool completely.

Seasoning raw pork chops with herbs and spices for grilling preparation.
Butter cookie dough with chocolate chips in mixing bowls, baking tray of cookies in progress, close-up of cookie preparation process.
Butter cookies with chocolate chips on a white plate.

PRO TIP:

For the best texture, make sure to use room temperature butter when creaming with the sugar. This helps the cookies spread evenly and results in a perfectly chewy center with crispy edges.

Storage and Reheating

Storage:  Store cooled cookies in an airtight container at room temperature for up to 5 days.

Reheating: To enjoy warm cookies, microwave them for 10-15 seconds.

Freezing: Freeze cookie dough balls on a baking sheet, then transfer to a zip-top bag and freeze for up to 3 months. Bake directly from frozen, adding an extra minute or two to the bake time.

Chewy chocolate chip cookies on a white plate, fresh out of the oven.

Additions & Substitutions

ADDITIONS:

  • Nuts: Add 1/2 cup of chopped walnuts or pecans for extra crunch.
  • Oats: Stir in 1/2 cup of old-fashioned oats for a heartier texture.

SUBSTITUTIONS:

  • Flour: If you don’t have freshly milled flour, regular whole wheat or all-purpose flour works too.
  • Butter: Unsalted butter can be used; just add a pinch more salt to the recipe.

FAQs about these Fresh Milled Flour Chocolate Chip Cookies:

Can I use regular flour instead of the freshly milled wheat flour?

Yes. You can substitute regular whole wheat flour or all-purpose flour if you do not have freshly milled flour. Freshly milled flour absorbs moisture differently, so you may notice a slight difference in texture when using store-bought flour.

How can I make these cookies softer?

Do not overbake them. The centers should still look slightly soft when you remove the cookies from the oven. They will continue to firm up as they cool.

Can I add nuts to the recipe?

Yes. Chopped walnuts or pecans are a great addition and add a little extra crunch to the cookies.

What Can I Serve with these Chocolate Chip Cookies made with Fresh Milled Flour?

Serve this Whole Wheat Chocolate Chip recipe with a cold glass of milk, hot coffee, hot cocoa, or put vanilla ice cream between two cookies and make an ice cream sandwich, yum!!

DID YOU MAKE THIS RECIPE?

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I’m excited for you to try these Whole Wheat Chocolate Chip Cookies! After you make it, please leave a rating to let me know your thoughts on it – I’m eager to hear if you loved it as much as we do!

Chocolate chip cookies on a while plate.

Whole Wheat Chocolate Chip Cookies (Fresh Milled Flour)

Vicky Hadley~Little Chef Within
Who says healthier cookies can’t taste just as amazing? These Whole Wheat Chocolate Chip Cookies are made with fresh milled flour, giving them a wholesome boost while still being soft, chewy, and packed with chocolatey goodness.
No ratings yet
Prep Time 10 minutes
Cook Time 10 minutes
Total Time 20 minutes
Course Dessert
Cuisine American
Servings 28 Cookies
Calories 139.2 kcal

Ingredients
  

  • 1 cup salted butter softened
  • 3/4 cup granulated sugar
  • 3/4 cup brown sugar packed
  • 2 large eggs
  • 2 teaspoons vanilla extract
  • 3 cups freshly milled soft white wheat flour
  • 1 teaspoon baking soda
  • 1/2 teaspoon salt
  • 1 cup semi-sweet chocolate chips
  • 1 cup semi-sweet chunks

Instructions
 

  • Preheat the oven to 375°F and line a baking sheet with parchment paper.
  • In the bowl of a stand mixer fitted with the paddle attachment, cream together the softened butter, granulated sugar, and brown sugar on medium speed until the mixture is light and fluffy.1 cup salted butter,3/4 cup granulated sugar,3/4 cup brown sugar.
  • Beat in the eggs, one at a time, and then stir in the vanilla extract.2 large eggs,2 teaspoons vanilla extract.
  • In a separate bowl, whisk together the freshly milled flour, baking soda, and salt. Gradually add this dry mixture to the wet ingredients, mixing until just combined.3 cups freshly milled soft white wheat flour,1 teaspoon baking soda,1/2 teaspoon salt.
  • Fold in the semi-sweet chocolate chips and chocolate chunks.1 cup semi-sweet chocolate chips,1 cup semi-sweet chunks.
  • Using a cookie scoop, drop spoonfuls of dough onto the prepared baking sheet, spacing them about 2 inches apart. Bake for 10-11 minutes, or until the edges are lightly golden, and the centers remain soft.
  • Allow the cookies to cool on the baking sheet for a few minutes before transferring them to a wire rack to cool completely.

Notes

TIP: For the best texture, make sure to use room temperature butter when creaming with the sugar. This helps the cookies spread evenly and results in a perfectly chewy center with crispy edges.

Nutrition

Calories: 139.2kcalCarbohydrates: 14.5gProtein: 0.5gFat: 9.1gSaturated Fat: 5.6gPolyunsaturated Fat: 0.3gMonounsaturated Fat: 2.4gTrans Fat: 0.3gCholesterol: 17.8mgSodium: 135.1mgPotassium: 46.8mgFiber: 0.5gSugar: 13.5gVitamin A: 205.8IUCalcium: 10.9mgIron: 0.5mg
Keyword chocolate chip cookies, cookies, freshly milled flour, whole wheat
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