Whole Wheat Chocolate Chip Cookies (Soft & Chewy Recipe)

Name: Whole Wheat Chocolate Chip Cookies (Soft & Chewy Recipe)
Prep time: 5 min
Cook time: 12 min
Total time: 17 min
Cuisine: American
Ingredients: 2 cups (240g) white whole wheat flour; 1 teaspoon baking soda; 1/2 teaspoon salt; 3/4 cup (170g) unsalted butter, melted and slightly cooled; 1 cup (200g) packed brown sugar; 1/2 cup (100g) granulated sugar; 2 large eggs, at room temperature; 2 teaspoons pure vanilla extract; 2 cups (340g) semi-sweet chocolate chips

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I'll be honest with you , I used to think whole wheat cookies meant giving up that melt-in-your-mouth, bakery-style texture I love. You know, the kind where chocolate chips stay gooey and the cookie itself is soft for days? I thought switching to whole wheat flour meant sacrificing all of that.

But then I discovered white whole wheat flour, and everything changed. These whole wheat chocolate chip cookies are just as soft, just as chewy, and just as irresistible as the classic version — with a little extra fiber and nutrition tucked inside. My kids, Logan and Ellie, can't tell the difference, and honestly, neither can most adults who try them.

The secret? White whole wheat flour has a milder flavor and lighter texture than regular whole wheat flour, so your cookies don't turn out dense or dry. Plus, I use melted butter and a higher ratio of brown sugar to keep these cookies soft and gooey even after they cool. Let's bake some cookies together!

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Can I Use Whole Wheat Flour Instead of All-Purpose Flour in Cookies?
5 Expert Tips for Soft, Chewy Whole Wheat Cookies
Why These Whole Wheat Cookies Are Different
INGREDIENTS FOR WHOLE WHEAT CHOCOLATE CHIP COOKIES
STEP-BY-STEP INSTRUCTIONS
STORAGE AND FREEZING
EXPERT TIPS FOR PERFECT WHOLE WHEAT COOKIES
INGREDIENT SUBSTITUTIONS & VARIATIONS
Best Gluten Free Chocolate Chip Cookies (Thick & Chewy)
Easy Coconut Date Balls Recipe (3 Ingredients, No-Bake)
FREQUENTLY ASKED QUESTIONS
NUTRITION BENEFITS OF WHOLE WHEAT COOKIES
SERVING SUGGESTIONS
📖 The Complete Recipe
Whole Wheat Chocolate Chip Cookies (Soft & Chewy Recipe)
💬 Reviews

Can I Use Whole Wheat Flour Instead of All-Purpose Flour in Cookies?

Yes, you can substitute whole wheat flour for all-purpose flour in cookies, but adjustments are needed for best results. Here's your quick reference guide:

Flour Type	Texture Result	Flavor Profile	Best Use Case	Adjustment Needed
White Whole Wheat Flour	Soft, tender (closest to AP)	Mild, slightly nutty	1:1 substitution, perfect for chocolate chip cookies	No adjustments needed
Regular Whole Wheat Flour	Denser, heartier	Strong wheat flavor	Use 50/50 with AP flour for balanced texture	Reduce flour by 2 tablespoon OR add 1-2 tablespoon liquid
Whole Wheat Pastry Flour	Light, delicate	Mild, wheaty	Great for soft cookies	1:1 substitution, sift first
All-Purpose Flour	Light, tender	Neutral	Traditional cookies	Standard recipe

Pro Tip: Whole wheat flour absorbs more liquid than all-purpose flour. If your dough looks dry, add 1-2 tablespoons of milk or water.

I always keep white whole wheat flour in my pantry now. King Arthur and Bob's Red Mill both make great versions, and you can find them in most grocery stores right next to the regular flour. The difference it makes in your cookies is incredible — all the wholesome goodness of whole grains without that heavy, dense texture.

5 Expert Tips for Soft, Chewy Whole Wheat Cookies

Whole wheat cookies often turn out dry or dense, but these proven techniques guarantee bakery-soft results every single time:

Use White Whole Wheat Flour - This lighter variety (also called "golden" whole wheat) has a milder flavor and softer texture than regular whole wheat flour. It's made from a different type of wheat that's naturally lighter in color and taste. King Arthur and Bob's Red Mill both make excellent versions that I use in my kitchen.
Never Overbake - Remove cookies when the tops still look slightly underdone and the edges are just golden brown. This is the hardest part for me because they look so pale! But trust me, whole wheat flour firms up more than all-purpose as it cools, so cookies that look "perfect" in the oven will be overbaked once cooled.
Use Melted Butter - Melted butter creates a chewier, fudgier texture compared to softened butter. The liquid fat coats the flour proteins differently, resulting in softer cookies. I learned this trick years ago, and it's been a game-changer for keeping cookies soft for days.
Increase Brown Sugar Ratio - Brown sugar contains molasses, which adds moisture and keeps cookies soft for days. I use at least 2 parts brown sugar to 1 part white sugar in this recipe. Sometimes I even use all brown sugar when I want an extra chewy batch.
Don't Overmix the Dough - Whole wheat flour develops gluten faster than all-purpose flour. Mix just until ingredients are combined to avoid tough, cakey cookies. I usually stop mixing the moment I can't see any more flour streaks.

Bonus Tip: Let cookies cool completely on the baking sheet for 15-20 minutes. This allows them to finish cooking gently with residual heat while maintaining a soft center.

Why These Whole Wheat Cookies Are Different

The Secret: White Whole Wheat Flour

The flour makes all the difference in this recipe. White whole wheat flour is made from hard white wheat instead of the more common hard red wheat used in regular whole wheat flour. It still contains the entire wheat kernel — the bran, germ, and endosperm — which means you get all the fiber, protein, and nutrients of whole grains.

But here's the beautiful part: it has a sweeter, milder flavor and a lighter color. When I first started baking with it, I was amazed at how it didn't have that strong, wheaty taste that can sometimes overwhelm cookies. My daughter Ellie, who's pretty picky about textures, couldn't even tell these weren't made with regular flour.

From a nutrition standpoint, you're getting about 4 grams of fiber per serving compared to virtually none in all-purpose flour. The whole grains also provide B vitamins, iron, and magnesium that are stripped away in refined flour. I feel better serving these to my kids as an after-school snack because I know they're getting a little nutritional boost along with their chocolate.

The Perfect Texture Formula

Getting soft, chewy cookies from whole wheat flour isn't about magic — it's about understanding how the ingredients work together. The melted butter creates those crispy edges and chewy centers we all love. Brown sugar adds moisture and that deep, caramel-like sweetness. And the chocolate chips? Well, they're just there to make life better.

I've tested this recipe at least a dozen times to get the proportions just right. Too much flour and the cookies turn out cakey. Not enough sugar and they're not quite sweet enough. But this combination? Perfect every time.

INGREDIENTS FOR WHOLE WHEAT CHOCOLATE CHIP COOKIES

Here's what you'll need to make about 24 cookies:

Dry Ingredients:

2 cups (240g) white whole wheat flour - Don't pack it into the measuring cup; spoon it in gently
1 teaspoon baking soda
½ teaspoon salt

Wet Ingredients:

¾ cup (170g) unsalted butter, melted and slightly cooled
1 cup (200g) packed brown sugar - I usually use light brown, but dark works too
½ cup (100g) granulated sugar
2 large eggs, at room temperature
2 teaspoons pure vanilla extract

Mix-ins:

2 cups (340g) semi-sweet chocolate chips - I like Ghirardelli or Guittard

The butter needs to be melted but not hot. If it's too warm, it can start cooking the eggs when you mix them in. I usually melt mine in the microwave in 30-second bursts, then let it sit on the counter for about 5 minutes while I measure everything else.

Room temperature eggs make a difference too. They blend more easily into the dough and create a smoother texture. If you forget to take them out ahead of time (which happens to me all the time), just place them in a bowl of warm water for about 5 minutes.

STEP-BY-STEP INSTRUCTIONS

Step 1
Preheat your oven to 350°F (175°C). Line two baking sheets with parchment paper or silicone baking mats. I prefer parchment paper because cleanup is so much easier, and the cookies slide right off.
Step 2
In a medium bowl, whisk together the white whole wheat flour, baking soda, and salt. Set this aside while you work on the wet ingredients. This is also a good time to get your kids involved if they're around — Logan loves being in charge of the whisk.
Step 3
In a large mixing bowl, combine the melted butter, brown sugar, and granulated sugar. Use a wooden spoon or rubber spatula to mix them together until they're well combined and the mixture looks smooth. It should take about 30 seconds of stirring.
Step 4
Add the eggs one at a time, mixing well after each addition. Then stir in the vanilla extract. The mixture should look glossy and slightly thickened at this point.
Step 5
Add the flour mixture to the wet ingredients in three additions, stirring gently after each addition. This helps prevent overmixing and keeps the cookies tender. Stop mixing as soon as you can't see any more flour streaks — a few small lumps are perfectly fine.
Step 6
Fold in the chocolate chips with a spatula. I always save a few extra chips to press into the tops of the cookies before baking. It makes them look bakery-perfect.
Step 7
Use a cookie scoop or spoon to drop rounded tablespoons of dough onto your prepared baking sheets, spacing them about 2 inches apart. They'll spread as they bake, so give them room. If you want uniform cookies, a 2-tablespoon cookie scoop is your best friend.
Step 8
Bake for 10-12 minutes, until the edges are just golden brown but the centers still look slightly underdone. This is the hardest part for me because they look so pale and soft! But remember, they'll continue cooking on the baking sheet after you remove them from the oven.
Step 9
Let the cookies cool on the baking sheet for 15-20 minutes before transferring them to a wire rack. This cooling time is important — it lets them set up without overbaking. I know it's tempting to dig in right away (believe me, I've burned my tongue more than once), but the wait is worth it.

Pro Tips While Making

Watch the oven carefully during the last few minutes of baking. Every oven is different, and whole wheat cookies can go from perfectly soft to overbaked in just a minute or two. I usually start checking at the 9-minute mark.

Don't flatten the dough before baking. These cookies will spread on their own to the perfect thickness. If you press them down, they'll end up too thin and crispy instead of soft and chewy.

Rotate your baking sheets halfway through baking if your oven has hot spots. I learned this the hard way after years of wondering why some cookies were darker than others.

Freeze extra dough for later. I usually scoop all the dough into balls, bake half, and freeze the rest on a baking sheet. Once they're frozen solid, I transfer them to a freezer bag. Then I can bake fresh cookies anytime by adding an extra minute or two to the baking time.

STORAGE AND FREEZING

These whole wheat chocolate chip cookies stay soft in an airtight container at room temperature for up to 5 days. I keep ours in a ceramic cookie jar on the counter, and they never last that long anyway.

If you want to freeze baked cookies, let them cool completely, then layer them in a freezer-safe container with parchment paper between layers. They'll keep for up to 3 months. To thaw, just leave them at room temperature for about 30 minutes, or warm them in a 300°F oven for 5 minutes.

Cookie dough freezes beautifully too. Scoop it into balls, freeze on a baking sheet until solid, then transfer to a freezer bag. You can bake frozen cookie dough straight from the freezer — just add 1-2 minutes to the baking time. This is my favorite trick for busy weeknights when the kids want something sweet.

EXPERT TIPS FOR PERFECT WHOLE WHEAT COOKIES

How to Keep Whole Wheat Cookies Soft

The key to keeping these cookies soft for days is proper storage and not overbaking them in the first place. Store cooled cookies in an airtight container with a slice of bread. The bread will gradually dry out, but it releases moisture that keeps the cookies soft. Replace the bread slice every couple of days.

You can also add a small piece of apple instead of bread if you want a subtle fruity aroma. I learned this trick from my grandmother, and it works like magic.

If your cookies do dry out, you can revive them by microwaving them for about 10 seconds with a damp paper towel nearby. The moisture from the paper towel will help soften them up again.

Common Mistakes to Avoid

Using regular whole wheat flour without adjustments - If you only have regular whole wheat flour on hand, substitute half with all-purpose flour for better texture. Using 100% regular whole wheat flour will give you denser, more cake-like cookies with a stronger wheat flavor.

Overbaking - This is the number one mistake I see people make with whole wheat cookies. They look underdone when they're actually perfect. Trust the recipe timing and pull them out when the centers still look soft.

Measuring flour incorrectly - Scooping flour directly from the bag packs it into the measuring cup, giving you too much flour. This makes cookies dry and tough. Always spoon flour into your measuring cup and level it off with a knife.

Skipping the cooling time - I know it's tempting to transfer cookies to a cooling rack right away, but letting them sit on the baking sheet for 15-20 minutes helps them develop that perfect chewy texture.

INGREDIENT SUBSTITUTIONS & VARIATIONS

Flour Substitutions

Can I use regular whole wheat flour? Yes, but your cookies will be denser and have a stronger wheat flavor. I recommend substituting only 50% of the white whole wheat flour with regular whole wheat flour for your first attempt. The other 50% should be all-purpose flour to maintain the soft texture.

Can I use all-purpose flour? Absolutely! This recipe works beautifully with all-purpose flour if you want traditional chocolate chip cookies. The texture will be slightly lighter, but still delicious.

Gluten-free option: I haven't perfected a gluten-free version of these cookies yet, but you might have luck with a 1:1 gluten-free flour blend like Bob's Red Mill or King Arthur. If you try it, check out our gluten-free chocolate chip cookies for more guidance.

Best Gluten Free Chocolate Chip Cookies (Thick & Chewy)

These thick and chewy gluten free chocolate chip cookies bake up with crisp golden edges, soft gooey centers, and that deep, rich flavor you remember from your favorite bakery. Chilling the shaped dough is the secret to amazing texture and flavor in every bite.

Mix-in Variations

The beauty of this recipe is how adaptable it is. Here are some of my favorite variations:

Chocolate lover's cookies: Use a combination of milk chocolate chips, dark chocolate chips, and white chocolate chips. The different types of chocolate create amazing flavor complexity.

Nutty cookies: Add 1 cup of chopped walnuts or pecans along with the chocolate chips. Toast the nuts first for extra flavor — just 5 minutes in a 350°F oven makes a huge difference.

Coconut date cookies: Replace half the chocolate chips with chopped dates and shredded coconut. This combination is naturally sweet and gives the cookies a chewy, almost caramel-like texture. If you love this flavor profile, you might also enjoy our coconut date balls.

Peanut butter swirl: Drop a spoonful of peanut butter into the center of each cookie dough ball before baking. It creates a gooey peanut butter center that pairs perfectly with the chocolate.

Healthier version: Use dark chocolate chips (70% cacao or higher) and reduce the granulated sugar to ⅓ cup. You can also add ¼ cup of ground flaxseed for extra fiber and omega-3s.

Easy Coconut Date Balls Recipe (3 Ingredients, No-Bake)

These easy 3-ingredient coconut date balls are naturally sweet, energy-packed no-bake treats that take just 5 minutes to make. Made with Medjool dates, almonds, and shredded coconut, these healthy snack balls are perfect for lunchboxes, pre-workout fuel, or satisfying your sweet tooth the wholesome way. Vegan, gluten-free, and refined sugar-free!

FREQUENTLY ASKED QUESTIONS

Why are my whole wheat cookies hard?

Hard, dry whole wheat cookies usually result from overbaking or using too much flour. Whole wheat flour absorbs more liquid than all-purpose flour and continues to firm up as cookies cool. Make sure you're measuring flour correctly (spoon it into the measuring cup, don't pack it), and pull cookies from the oven when the centers still look slightly underdone. They should be barely set in the middle with golden edges.

Can I use regular whole wheat flour instead of white whole wheat?

Yes, you can substitute regular whole wheat flour, but I recommend mixing it 50/50 with all-purpose flour for the best texture. Regular whole wheat flour has a stronger flavor and denser texture than white whole wheat flour. If you use 100% regular whole wheat, your cookies will be heartier and more cake-like with a pronounced wheat taste. Some people love this, but it's not the same soft, chewy cookie texture.

How do you store whole wheat cookies?

Store completely cooled cookies in an airtight container at room temperature for up to 5 days. Layer them with parchment paper if stacking, and add a slice of bread to the container to keep them soft. The bread releases moisture that prevents cookies from drying out. You can also freeze baked cookies for up to 3 months in a freezer-safe container.

Can I freeze the cookie dough?

Absolutely! Cookie dough freezes beautifully for up to 3 months. Scoop the dough into balls and freeze them on a baking sheet until solid, then transfer to a freezer bag. You can bake frozen cookie dough directly from the freezer without thawing — just add 1-2 minutes to the baking time. This is perfect for those moments when you want fresh-baked cookies but don't want to make a full batch.

Are whole wheat cookies healthier than regular cookies?

Whole wheat cookies provide more fiber, protein, vitamins, and minerals than cookies made with all-purpose flour. White whole wheat flour contains about 4 grams of fiber per serving compared to virtually none in refined flour. According to WebMD, whole wheat also provides B vitamins, iron, and magnesium. That said, these are still cookies with butter and sugar, so they're best enjoyed as an occasional treat. But if you're going to have a cookie, getting some extra nutrition is a nice bonus.

What is white whole wheat flour?

White whole wheat flour is made from hard white wheat instead of the hard red wheat used in regular whole wheat flour. It still contains the entire wheat kernel (bran, germ, and endosperm), so you get all the nutritional benefits of whole grains. The difference is that white wheat has a sweeter, milder flavor and lighter color that works beautifully in cookies without the dense texture or strong wheat taste.

NUTRITION BENEFITS OF WHOLE WHEAT COOKIES

I'm not going to pretend these are health food — they're cookies, after all, and they're meant to be enjoyed as a treat. But using white whole wheat flour does give you some nutritional benefits compared to traditional chocolate chip cookies made with all-purpose flour.

Whole wheat flour provides significantly more fiber than refined flour. Each cookie has about 1.5-2 grams of fiber, which helps with digestion and keeps you feeling satisfied. The whole grain also contains B vitamins like niacin and thiamin, plus minerals like iron, magnesium, and zinc that are removed during the refining process.

The beauty of white whole wheat flour is that you get these nutritional benefits without compromising on taste or texture. My kids have no idea they're eating something with a little extra nutrition — they just know the cookies taste amazing.

Are these an everyday breakfast food? No. But when you want a sweet treat, it's nice knowing you're choosing a slightly more wholesome option. Plus, the satisfaction from the fiber means you might be happy with one or two cookies instead of eating half the batch.

SERVING SUGGESTIONS

These whole wheat chocolate chip cookies are perfect for so many occasions. I pack them in Logan and Ellie's lunchboxes as a special treat (they trade them for all sorts of things at school). They're wonderful for holiday cookie exchanges, bake sales, or gifts for neighbors and teachers.

Serve them slightly warm with a cold glass of milk for the ultimate after-school snack. The chocolate gets all melty again, and they taste like they just came out of the oven. On cozy weekend mornings, I sometimes crumble a cookie over vanilla ice cream for dessert.

They're also perfect for sharing at family gatherings. I always bring a batch to my mom's house when we visit, and they disappear within minutes. Last Thanksgiving, I made a triple batch and still ran out before dinner was over.

For a special presentation, stack them in a clear jar tied with ribbon. It makes a lovely homemade gift that feels personal and thoughtful. I keep a few batches of frozen cookie dough in my freezer so I can bake fresh cookies whenever I need a last-minute gift.

These whole wheat chocolate chip cookies have become one of my most-requested recipes from friends and family. The combination of soft, chewy texture, rich chocolate flavor, and the subtle nuttiness from white whole wheat flour creates something really special. You get all the comfort of classic chocolate chip cookies with a little extra nutrition tucked inside.

I hope these become a favorite in your kitchen too. There's something magical about the smell of cookies baking and the joy of sharing them with people you love. Save this recipe, give it a try, and let me know how they turn out for you! If you love these as much as we do, you might also enjoy browsing through our other cookie recipes for more family-friendly treats.

Happy baking!

Can I Use Whole Wheat Flour Instead of All-Purpose Flour in Cookies?

5 Expert Tips for Soft, Chewy Whole Wheat Cookies