Ultimate Whole Wheat Chocolate Chunk Cookies: A Perfect Blend of Health & Indulgence
After a dedicated week of testing and refining, I am thrilled to share the recipe for what I believe are truly exceptional whole wheat chocolate chunk cookies. While they might appear to be just another variation of chocolate chip or chocolate chunk cookies, the journey to perfecting this recipe has resulted in a cookie that stands out for its unique blend of wholesome ingredients and irresistible flavor. These aren’t just good; they’re *really* good, delivering a satisfying chewiness and a depth of flavor that’s hard to beat.
My quest for the perfect whole wheat cookie began with inspiration from Kim Boyce’s acclaimed book, Good to the Grain. Her recipes, often featuring 100% whole wheat flour, beautifully highlight the robust, earthy notes of wheat. While I deeply appreciate the authentic flavor of whole grains, my goal for this particular cookie was to achieve a slightly more subtle wheat presence—a harmonious balance where the whole wheat flour contributes to the cookie’s character without overpowering the other delightful components. To achieve this, I opted for a blend of all-purpose and whole wheat flour, striking a delicious middle ground.
Beyond the flour, I experimented with various add-ins to elevate the cookie experience. The idea of incorporating toffee was a spontaneous, last-minute decision, an excellent way to utilize some leftover Heath Bars from Halloween. While the toffee adds a fantastic caramelized crunch and an extra layer of sweetness, rest assured that these cookies remain utterly delicious even if you choose to omit it. However, one ingredient I strongly recommend keeping are the nuts. Toasted pecans or walnuts provide a crucial textural contrast and a nutty depth that beautifully offsets the sweetness of the chocolate and sugars, making each bite more complex and satisfying.
Choosing Your Chocolate: Chips vs. Chunks for the Perfect Cookie
When it comes to the star ingredient – chocolate – you have a few options that can subtly change your cookie’s outcome. I made batches using both extra dark chocolate chips and finely chopped Callebaut chocolate chunks (a truly worthwhile indulgence!). Interestingly, cookies made with chocolate chips tended to spread less, which is often the case. Furthermore, I found that I could incorporate a higher quantity of chocolate into each cookie when using chips, leading to an even more chocolate-packed experience. Whether you prefer the classic melt of chips or the dramatic pockets of chunks, choose a high-quality dark chocolate to truly make these cookies shine. The bitterness of dark chocolate provides a wonderful counterpoint to the sweetness of the dough, creating a balanced and sophisticated flavor profile.
The Wholesome Advantage of Whole Wheat Flour
Opting for whole wheat flour in your baking is a fantastic way to introduce more fiber and nutrients into your diet without sacrificing flavor. Unlike refined all-purpose flour, whole wheat flour retains the bran and germ of the wheat kernel, which are packed with vitamins, minerals, and dietary fiber. This not only makes for a more nutritious cookie but also contributes to a unique texture and a more complex, earthy flavor. In this recipe, the Hodgson Mill Whole Wheat Flour (or “Graham Flour”) was chosen for its distinct taste that perfectly complements the rich chocolate and crunchy nuts. It adds a rustic charm that distinguishes these cookies from their all-purpose counterparts, giving them a comforting, homemade feel that health-conscious bakers and foodies alike will appreciate.
The Secret to Superior Cookies: Chilling the Dough
While patience might not be every baker’s virtue, chilling this cookie dough is a step you won’t want to skip. The scientific magic behind chilling cookie dough is twofold: it allows the flour to fully hydrate, leading to a more tender and cohesive texture, and it gives the flavors a chance to meld and deepen over time. The result? A more nuanced, richer flavor profile that simply can’t be achieved with immediate baking. Furthermore, chilling the dough significantly reduces cookie spread during baking, ensuring your cookies maintain a beautiful, thick shape with satisfyingly chewy centers and slightly crisp edges. An overnight chill is ideal, transforming good dough into truly great dough.
Recipe: Jumbo Whole Wheat Toffee Chocolate Chunk Cookies

Jumbo Whole Wheat Toffee Chocolate Chunk Cookies
Anna
Pin Recipe
Ingredients
- 8 tablespoons unsalted butter (114 grams), softened
- ⅓ cup tightly packed dark brown sugar (70 grams)
- ½ cup granulated sugar (100 grams)
- 1 large egg cold, for better texture
- 1 teaspoon vanilla bean paste or vanilla extract
- ¾ teaspoon baking powder
- ½ teaspoon baking soda
- ¾ teaspoon salt (e.g., Morton Kosher, which measures like table salt)
- ¾ cup all-purpose flour (100 grams)
- ⅔ cup Hodgson Mill Whole Wheat Flour or “Graham Flour” (90 grams)
- 1 ⅓ cup extra dark chocolate chips or chunks
- 6 mini Heath Bars chopped, optional for toffee crunch
- ⅔ cup toasted and chopped pecans or walnuts
Instructions
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Hold off on preheating your oven for now. This cookie dough truly benefits from a chilling period, which enhances flavor and texture. While you can bake immediately, chilling helps prevent excessive spreading.
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In a large mixing bowl, use an electric mixer to beat the softened butter on medium speed until creamy. Incorporate both the dark brown sugar and granulated sugar, beating until the mixture is light and fluffy. Scrape down the sides of the bowl as needed, then beat in the cold egg and vanilla. Once the egg is fully blended, mix in the baking powder, baking soda, and salt.
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Switch to hand mixing or a spatula. Gently stir in both the all-purpose and whole wheat flours until just combined and no dry streaks remain. Be careful not to overmix. Finally, fold in the chocolate chips or chunks, the chopped Heath Bars (if using for that extra crunch), and the toasted nuts until evenly distributed throughout the dough.
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Using a generously heaping tablespoon or a medium cookie scoop, form large mounds of dough and arrange them on a foil-lined plate. Cover the plate tightly with plastic wrap and refrigerate for at least 8 hours, or ideally, overnight. This chilling step is crucial for the best flavor and texture.
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When ready to bake, preheat your oven to 350 degrees F (175 degrees C). Line two baking sheets with regular aluminum foil (avoid nonstick or parchment for these cookies, as regular foil helps with browning).
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Place the chilled dough mounds about 3 inches apart on the prepared baking sheets to allow for spreading. Gently press down the tops of each dough mound slightly to flatten them and ensure even baking.
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Bake on the center rack of your preheated oven for approximately 15 minutes. The cookies are done when the edges appear set and are lightly browned, and the centers still look slightly soft. Baking time may vary slightly depending on your oven.
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Allow the freshly baked cookies to cool on the baking sheet for about 4 minutes. This resting period allows them to firm up slightly before being moved. Then, carefully transfer them to a wire rack to cool completely. Enjoy the warm, gooey goodness, or let them cool for perfect texture!
Notes
Chilling the Dough: While technically optional, chilling this dough overnight significantly improves the flavor development and helps prevent the cookies from spreading too much, resulting in a thicker, chewier final product. Don’t skip it for the best results!
Toasting Nuts: To toast your pecans or walnuts, spread them in a single layer on a baking sheet. Bake in a 350°F (175°C) oven for about 6 to 8 minutes, or until they become fragrant and lightly browned. Keep a close eye on them, as nuts can burn quickly.
Ingredient Specifics: I’ve mentioned Hodgson Mill brand graham flour because some whole wheat flours have a stronger “wheat-y” flavor. This brand provides a pleasant, balanced whole wheat taste. For salt, exact measurements can vary between brands, even for “coarse” varieties. Morton Kosher salt, for example, measures similarly to table salt. Other brands with larger crystals might require a higher quantity to achieve the same seasoning. Sticking with Morton allows for easy interchangeability with recipes calling for table salt, ensuring consistent flavor.
Expert Tips for Cookie Perfection
Achieving the perfect whole wheat chocolate chunk cookie goes beyond just following the recipe; a few key techniques can make all the difference. Firstly, ensure your butter is at room temperature – not melted, not too cold. This allows it to cream properly with the sugars, creating a light, airy base for your dough. When mixing in the dry ingredients, stop as soon as the flour is just incorporated to avoid developing too much gluten, which can lead to tough cookies. Overmixing is a common pitfall that robs cookies of their tender chewiness.
Another crucial tip is to always use a cold egg. A cold egg helps to keep the butter from melting too quickly when it interacts with the other ingredients, especially important when creaming. The slight temperature difference contributes to a more stable emulsion, which is the foundation of a well-structured cookie. Finally, pay close attention to your oven. Ovens can vary significantly in temperature, so investing in an oven thermometer can ensure your baking environment is consistently at the right heat, preventing burnt edges or undercooked centers. Adjust baking times slightly based on your oven’s performance to achieve that ideal golden-brown edge and soft, chewy middle.
Customization and Storage for Your Whole Wheat Masterpiece
These whole wheat chocolate chunk cookies are wonderfully adaptable. Feel free to experiment with different types of chocolate, such as milk chocolate or white chocolate, or even a mix for varied sweetness. If you’re not a fan of pecans or walnuts, try almonds, hazelnuts, or even pepitas for a unique flavor twist. For an added layer of flavor, consider including a pinch of cinnamon or a dash of espresso powder with your dry ingredients. Dried cranberries or cherries can also introduce a delightful tartness, beautifully complementing the rich chocolate.
To store your freshly baked cookies, allow them to cool completely on a wire rack before transferring them to an airtight container. They will stay fresh at room temperature for up to 3-4 days. For longer storage, you can freeze the baked cookies for up to 3 months. Simply thaw them at room temperature or warm them gently in the oven for a freshly baked experience. The raw cookie dough can also be frozen; scoop mounds onto a baking sheet, freeze until solid, then transfer to a freezer-safe bag for up to 2 months. When ready to bake, place the frozen dough balls directly on a baking sheet and add a few extra minutes to the baking time.
I am incredibly proud of these jumbo whole wheat chocolate chunk cookies. They embody the perfect balance of wholesome ingredients and indulgent flavors, proving that healthy can indeed be delicious. Whether you’re making them for a special occasion or simply to treat yourself, I’m confident they’ll become a cherished recipe in your collection. Happy baking!