Chocolate Chip Cookies with Whole Wheat Flour

These whole wheat chocolate chip cookies bake up soft, chewy, and full of chocolate, with the deeper flavor that comes from fresh milled soft wheat flour. Brown sugar, butter, vanilla, and plenty of semisweet chocolate chips give them the classic chocolate chip cookie texture and flavor, while the fresh milled flour adds a warm, wholesome taste without making the cookies heavy. If you enjoy baking with fresh milled flour and chocolate chips, you may also like my Whole Wheat Banana Muffins with Chocolate Chips.

I wanted a 100% whole wheat chocolate chip cookie that held its shape, stayed chewy in the middle, and still tasted like the classic cookies our family loves. These are made with soft wheat berries milled into fresh flour, then the dough is rested and chilled so the flour has time to hydrate before baking. For another chocolate recipe with milled wheat, try my Chocolate Milled Wheat Sourdough Quick Bread Recipe.

This post contains affiliate links, which means I make a small commission at no extra cost to you. See my full disclosure here.

Quick Look at This Recipe

Prep time: 15 minutes
Bake time: 10 to 12 minutes
Total time: About 1 hour 30 minutes, including chilling
Servings: About 24 cookies
Texture: Chewy centers, lightly crisp edges, and plenty of chocolate chips
Best served: Slightly warm with milk, coffee, or packed in a simple homemade dessert tray

Why You’ll Love This Recipe

These cookies are made with 100% whole wheat flour, but they still feel like a classic chocolate chip cookie. The soft milled wheat flour gives them a deeper flavor, while the brown sugar helps keep the centers chewy.

I also like that this recipe does not use cornstarch. The extra spoonful of flour, the egg yolk, the dough rest, and the chill time all work together to help the cookies hold their shape.

For another chocolate chip-style bake with a different texture, my Sourdough Discard Cherry Chocolate Chip Quick Bread is a nice option!

Ingredients

1 cup unsalted butter, softened but still cool
1 cup packed brown sugar
⅓ cup granulated sugar
1 large egg
1 egg yolk
2 teaspoons vanilla extract
2 ½ cups plus 1 tablespoon soft milled wheat flour, 367 g
1 teaspoon baking soda
½ teaspoon baking powder
¾ teaspoon salt
1 ½ cups semisweet chocolate chips or chocolate chunks

Ingredient Notes

Soft milled wheat flour works best for these cookies because soft wheat is better suited for tender baked goods. I mill the flour as finely as possible, then let it cool before adding it to the cookie dough if it feels warm from the mill.

Brown sugar gives these cookies a chewy texture and a deeper flavor. I use more brown sugar than granulated sugar for that reason.

Granulated sugar helps the edges bake up lightly crisp while still keeping the centers soft.

Butter should be softened but still cool. If the butter is too warm, the cookie dough may spread more in the oven.

The extra egg yolk adds richness and chew without making the dough too wet.

Baking soda and baking powder work together to help the cookies rise, spread just enough, and bake with a good texture.

Semisweet chocolate chips are my favorite here, but chocolate chunks also work well if you want bigger pockets of chocolate.

Equipment

Grain mill
Large mixing bowl
Medium mixing bowl
Hand mixer or stand mixer
Measuring cups and spoons
Kitchen scale
Spatula
Cookie scoop
Parchment paper
Baking sheet
Cooling rack

How to Make Chocolate Chip Cookies with Whole Wheat Flour

Mill your soft wheat berries as finely as possible. If the flour feels warm after milling, let it cool completely before using it in the cookie dough. Fresh milled flour can absorb moisture differently than store-bought flour, so weighing the flour is the most reliable option for this recipe

Step 1: In a medium bowl, whisk together the soft milled wheat flour, baking soda, baking powder, and salt. Set the dry ingredients aside while you mix the butter and sugars.

Step 2: In a large mixing bowl, cream the softened butter, brown sugar, and granulated sugar together for about 2 minutes, until the mixture is well combined and slightly fluffy. The butter should not look melted or greasy. If it does, chill the bowl for a few minutes before moving on.

Step 3: Add the egg, egg yolk, and vanilla extract. Mix until smooth. Scrape down the sides of the bowl so everything is evenly combined.

Step 4: Add the dry ingredients to the wet ingredients and mix just until the flour is fully combined. Do not overmix the cookie dough. Once the flour disappears, stop mixing.

Step 5: Fold in the semisweet chocolate chips or chocolate chunks with a spatula. At this point, the dough should be thick but scoopable. Let the cookie dough rest for 20 minutes. This gives the fresh milled flour time to absorb the moisture in the dough. This step helps improve the texture and keeps the cookies from feeling gritty.

Step 6: Scoop the dough into tall mounds, about 2 tablespoons each. Do not flatten the dough balls. Place the scooped dough on a parchment-lined baking sheet or plate and chill for at least 1 hour. For thicker cookies, chill for 2 to 4 hours.

Step 7: Preheat the oven to 350°F. Place the chilled cookie dough balls on a parchment-lined baking sheet, leaving space between each one. Bake for 10 to 12 minutes, or until the edges are set and lightly golden but the centers still look slightly soft.

Step 8: Let the cookies cool on the baking sheet for 10 minutes before moving them to a cooling rack. They will continue to set as they cool.

Tips for the Best Whole Wheat Chocolate Chip Cookies

Use soft wheat berries for the best texture. Hard wheat can make cookies heavier.

Do not skip the dough rest. Fresh milled flour needs time to absorb moisture.

Chill the scooped dough so the cookies bake thicker and do not spread too much.

Scoop the dough into tall mounds instead of flattening them.

Pull the cookies from the oven when the centers still look slightly soft. Overbaking can make whole wheat cookies dry.

Let the cookies cool on the baking sheet before moving them so the centers finish setting.

How to Keep Whole Wheat Chocolate Chip Cookies from Baking Flat

The best way to keep whole wheat chocolate chip cookies from baking flat is to use cool softened butter, weigh the flour, rest the dough, and chill the scooped cookie dough before baking. Fresh milled flour also needs time to absorb moisture, so the rest and chill time are especially important in this recipe.

If your cookies still spread too much after testing, add a little more flour next time. I would increase the flour to 2 ⅔ cups, or about 381 g total, for the next batch.

Can I Use Store-Bought Whole Wheat Flour?

Yes, you can use store-bought whole wheat flour, but the cookies may have a slightly different texture. Fresh milled soft wheat flour usually gives these cookies a lighter, fresher taste.

If using store-bought whole wheat flour, start with the same amount by weight and watch the dough texture. It should be thick enough to scoop and hold its shape.

How to Store These Cookies

Store cooled cookies in an airtight container at room temperature for 3 to 4 days.

You can also freeze the baked cookies for longer storage. Let them cool completely, then place them in a freezer-safe bag or container.

For fresh cookies later, freeze the scooped dough balls before baking. Bake from frozen at 350°F, adding 1 to 2 extra minutes if needed.

What to Serve with Chocolate Chip Cookies

These cookies are simple enough for an everyday dessert, but they also fit well on a homemade snack tray.

For a fresh milled flour snack spread, serve them with Homemade Milled Wheat Sourdough Graham Crackers, fruit, and milk. If you want to keep the from-scratch theme going, they are also a good recipe to make after learning How To Make Easy Homemade Butter From Raw Milk.

Frequently Asked Questions About Chocolate Chip Cookies with Whole Wheat Flour