My Most Requested Recipe: My Whole Wheat Chocolate Chip Cookies

These Whole Wheat Chocolate Chip Cookies are soft, chewy, and packed with rich dark chocolate. Made with whole wheat flour and coconut sugar, they offer a wholesome twist on a classic treat—without sacrificing flavor! Get the recipe and pro tips for perfect cookies every time.

written by Texas

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Healthy-ish Whole Wheat Chocolate Chip Cookies You’ll Love

The Best Whole Wheat Chocolate Chip Cookies: Years in the Making

There’s something magical about the perfect chocolate chip cookie—the warm, melty chocolate, the crisp edges, the soft, chewy center. But what if you could enjoy all of that while using more wholesome ingredients? That’s exactly what I set out to create, and after years of testing, tweaking, and perfecting, I’m sharing my most requested recipe: my Whole Wheat Chocolate Chip Cookies.

Why Whole Wheat? Why Coconut Sugar? Why Dark Chocolate?

When I first set out to make a “healthier” chocolate chip cookie, I knew I didn’t want to sacrifice taste or texture. This is still a cookie recipe—it’s meant to be enjoyed! But by using a few simple swaps, I found a way to make them just a little more nutritious without losing that indulgent quality.

• Whole Wheat Flour – Unlike white flour, whole wheat flour keeps the bran and germ, meaning it’s richer in fiber and nutrients. It adds a slight nuttiness and chewiness to the cookies, which I absolutely love.
• Coconut Sugar – A less processed sweetener with a caramel-like depth, coconut sugar has a lower glycemic index than white sugar, helping to prevent those sugar spikes.
• Dark Chocolate Chips – With a higher cocoa content, dark chocolate brings deep, rich flavor while also offering antioxidants.

The Texture & Flavor: What to Expect

If you’re worried that using whole wheat flour will make these cookies dense or dry—fear not! These cookies are soft, chewy in the center, and have just the right amount of crispness around the edges. The coconut sugar gives them a hint of caramel, and the dark chocolate chips melt into perfect pools of rich chocolate.

Pro Tips for the Perfect Cookie

Here are a few things I’ve learned over the years to make sure these cookies turn out perfectly every single time:

• Use room temperature ingredients. This ensures even mixing and better texture.
• Don’t overmix the dough. Overworking the flour can make cookies tough instead of tender.
• Chill the dough. Letting the dough rest in the fridge for at least 30 minutes deepens the flavor and helps prevent excessive spreading.
• Bake until just golden. Cookies continue to cook as they cool, so take them out when they look slightly underbaked in the center.

How to Serve & Store

These cookies are best enjoyed fresh out of the oven with a glass of cold milk (or your favorite dairy-free alternative). They store beautifully in an airtight container for up to a week, and if you want to keep some on hand for emergencies (because cookie cravings are real), you can freeze the dough in pre-portioned scoops and bake as needed.

The Recipe: Whole Wheat Chocolate Chip Cookies

Ingredients:

• 1 cup/227g (2 sticks) unsalted butter, softened
• 3/4 cup/140g coconut sugar (or raw sugar)
• 3/4 cup/142g brown sugar
• 2 large eggs yolks
• 1 teaspoons pure vanilla extract
• 1 1/4 cups/156g unbleached AP flour (or regular All-Purpose flour)
• 1/2 cup/65g whole wheat flour
• 1/2 cup/65g wheat germ (or whole wheat flour)
• 1 teaspoon baking soda
• 1 teaspoon sea salt
• 2 cups dark chocolate chips (or mix of semi-sweet, milk chocolate and/or dark chocolate)

Instructions:

1. In a large mixing bowl, cream together the butter, coconut sugar, and brown sugar until light and fluffy.
2. Beat in the egg yolks one at a time, then add the vanilla extract.
3. In a separate bowl, whisk together the whole wheat flour, baking soda, and salt.
4. Gradually add the dry ingredients to the wet ingredients, mixing until just combined.
5. Fold in the dark chocolate chips.
6. Optional Step: Cover the dough and chill in the refrigerator for at least 30 minutes (or up to 24 hours for even better flavor).
7. Preheat the oven to 375°F (190°C) and line a baking sheet with parchment paper.
8. Scoop the dough into tablespoon-sized balls and place them on the baking sheet, leaving space for spreading.
9. Bake for 15-17 minutes, or until the edges are golden brown and the centers look slightly underdone.
10. Let them cool on the baking sheet for 5 minutes before transferring to a wire rack to cool completely.

Recipe Card: 

Final Thoughts

This recipe has been a labor of love, and I’m so excited to finally share it with you. Whether you’re baking for your family, meal prepping a batch to keep in the freezer, or just looking for a way to make your favorite treat a little more wholesome, I hope these Whole Wheat Chocolate Chip Cookies become a staple in your kitchen too.

Let me know if you try them! I’d love to hear how they turn out and if they become a favorite in your home, just like they have in mine. Happy baking!

Whole Wheat Chocolate Chip Cookies Recipe

Whole Wheat Chocolate Chip Cookies

Prep Time: 10 min | Cook Time: 15 min | Servings: 24 cookies

Ingredients:

• 1 cup (227g) unsalted butter, softened
• 3/4 cup (140g) coconut sugar
• 3/4 cup (142g) brown sugar
• 2 large egg yolks
• 1 tsp vanilla extract
• 1 1/4 cups (156g) unbleached AP flour
• 1/2 cup (65g) whole wheat flour
• 1/2 cup (65g) wheat germ (or extra whole wheat flour)
• 1 tsp baking soda
• 1 tsp sea salt
• 2 cups dark chocolate chips

Instructions:

1. Cream butter, coconut sugar, and brown sugar until fluffy.
2. Beat in egg yolks and vanilla.
3. Mix dry ingredients in a separate bowl, then combine with wet ingredients.
4. Fold in dark chocolate chips.
5. Chill dough for 30 minutes (optional).
6. Preheat oven to 375°F (190°C) and line a baking sheet.
7. Scoop dough onto sheet and bake for 15-17 min until golden.
8. Cool on a wire rack before serving.