These Whole Wheat Chocolate Fudge Cookies are everything you want in one rich, fudgy cookie!

*Angels singing*
Chocolate chocolate double chocolate and a lot of sugar too. I’m in heaven.
I have been obsessed with these cookies ever since Lindsay and Heidi blogged about them. So thick! So fudgy!! So chocolatey!!!
I already have a double chocolate cookie recipe on the blog (which is totally one of my faves), but I wanted that big puffy cookie that Lindsay promised.
Problem was, I had already melted my butter when I realized I was out of white flour. I couldn’t believe it was possible for me to run out of flour (I like to be prepared for anything in the kitchen) but my daughter requested pancakes for breakfast a few days before and, well, I wanted pancakes too. Flour = devoured.

I considered dropping my desire for cookies, but I had already come this far and was really planning on having a chocolate fudge cookie in my mouth soon. I decided to do the unthinkable – replace the white flour entirely with whole wheat flour.
Whole wheat flour can make baked goods a little dry, so I decreased the overall amount of flour and used brown sugar to pump up the moisture. I like to use my favorite North Dakota Mills flour when baking with whole wheat.

If you don’t care for the texture of whole wheat in your baking I recommend giving this one a try or going with a white whole wheat.
As I mentioned in my post about the many ways to make chocolate chip cookies, you are welcome to bake these whole wheat chocolate fudge cookies right after mixing the dough. Chilling the dough, however, allows them to stay nice and puffy in the oven without spreading out all over the place. And we all know by now that I was after a puffy cookie.
Did I mention I’m trying to get in better shape? I’m my own worst enemy.

If you make this recipe, be sure to rate it, leave a comment, or tag #theliveinkitchen on Instagram!

Whole Wheat Chocolate Fudge Cookies
Ingredients
- 1 cup (2 sticks) butter
- 1 cup granulated sugar
- ½ cup dark brown sugar
- 2 teaspoons pure vanilla extract
- 2 large eggs
- ½ cup unsweetened cocoa powder
- 2 cups whole wheat flour
- 1 teaspoon baking soda
- ½ teaspoon salt
- 2 cups semisweet chocolate chips
Instructions
- Place one stick of butter on the kitchen counter to soften. Place the other stick of butter in a microwave safe bowl and melt completely in the microwave. Allow the butter to cool to a semisoft texture either on the counter or in the refrigerator, about 30 minutes.
- In the bowl of a stand mixer fitted with the paddle attachment, cream the softened butter, microwaved butter, and both sugars until fluffy. Add vanilla and eggs and mix briefly until just incorporated.
- In a separate bowl, whisk together cocoa powder, flour, baking soda, and salt. Add the flour mixture to the butter mixture and combine until you cannot see any more dry flour. The dough should be sticky but you should be able to touch it with your hands without it being too messy. Stir in chocolate chips.
- Cover the top of the bowl tightly with plastic wrap and allow the dough to rest in the refrigerator for 30 minutes or up to 2 days.
- When you’re ready to bake the cookies, preheat the oven to 350ºF. Roll the dough into balls slightly larger than a golf ball and place two inches apart on a baking sheet lined with parchment paper or a Silpat. Bake 8-9 minutes, depending on how cold your dough is. The cookies should be puffy and soft. Allow to cool on the baking sheet for 5-10 minutes before transferring to a cooling rack to cool completely (or be devoured).
liz | carpé season says
Made Lindsay’s version last weekend because I couldn’t hold out anymore! This post makes me want to whip up another batch tonight…you know, to celebrate…because it’s Friday!
Lindsay Moe says
Yes! I still want to try the original and see how it matches up to the whole wheat version!
Stephanie @ Girl Versus Dough says
I am thisclose to licking my computer screen. SO MUCH YUM.
Lindsay Moe says
You definitely need to try them!!
Kendra says
Now those look like they would have been worth the 45 minute trip when I was having a chocolate attack. Can’t wait to try them.
Lindsay Moe says
Ummm, yeah, I wasn’t kidding!
Alex says
These are great! I refrigerated the dough for about a half hour (as long as I could wait), and they came out perfect! Thanks. I will definetly be having fun with this recipe. 🙂
Lindsay Moe says
Thanks Alex, I’m glad you enjoyed them!
peggy says
I’m sure I’m not the only one to appreciate that the only measuring utensils needed for this recipe are a half cup measure and a teaspoon. That was great! Fudge cookies with little cleanup! Thanks <3
Dawn says
Love love love this recipe. I had wheat flour on hand that I didn’t know what to do with and this was perfect!
I buttered muffin tins and used an ice cream scoop because I like the uniformity. I love the cookies to cool before removing them from the pans.
The cookies came out like mini brownie bites.
Dawn says
Oops, I forgot to 5 star this recipe. Moderator please do this for me.
Lindsay Moe says
Killer idea! Thanks for sharing!
Ruth Music says
I would have been a lot more successfu had I read through the recipe before making it. The stick of butter that I was instructed to leave sitting on the counter was still on the counter when all was blended. Changing the directions to “cream all of the butter” would have helped. Fortunately, the cookies were still very good when I added the counter butter in at the end!
Lindsay Moe says
I’m so sorry you had trouble with the recipe. I have updated the wording to hopefully eliminate this issue. I’m glad you were still able to enjoy the cookies!
Pooja says
Such a great recipe, thank you thank you so much… I just made with a little less sugar as we like a little less sweet and the cookies were awesom so that my husband wants more n more. I made these last Friday and all of the cookies got over in less than 3 days 😀 baking more today 🙂
Lindsay Moe says
Yay! I totally support making cookies more than once a week.
Mamakitty says
Do you happen to know the “scientific” reason for melting half of the butter and letting it slightly harden? It seemed like my cookies were too crispy on the bottom, like the butter sort of fell to the bottom. Maybe the butter didn’t solidify enough? I have never seen a recipe that instructs you to do something like that. (I also over-cooked the first batch… Hard to tell when a chocolate cookie is done because it can’t get much browner than it naturally is in its raw state! :-D)
Lindsay Moe says
It does affect the texture. If they were too crisp on the bottom I would first check your oven temp and that the rack was in the middle of the oven, then maybe let it cool and solidify a bit more before mixing. This is definitely a cookie that needs to bake by time, not sight, they will appear a little underdone when you pull them out but firm up as they cool.
Vickie jones says
Can you use no calorie sweetener in place of sugar ?
Lindsay Moe says
I don’t use no calorie sweeteners, so I really can’t say for sure. I imagine the texture would come out a little different but would still taste good. If you experiment with it and they seem dry, perhaps add an extra egg yolk.
Isabella says
I’ve made this recipe biweekly since February, haha! It’s a great way to procrastinate on school work and it yields delicious results. They genuinely are the best cookies, and the longer the dough is left in the fridge the more chunky and soft they are after baked. I’ve recently been adding toffee chips in addition to the chocolate chips, and they are a neighborhood favorite. Thank you for this recipe!
Lindsay Moe says
This comment is the best! I’m so glad you’re loving this recipe, the toffee chips sound like a great idea!!
Carly says
These were sooooo delicious. I made a half batch because I just wanted a little treat, and they came out perfectly. I followed the directions exactly (cut back maybe a couple tablespoons of sugar) and they were puffy, soft, and rich. Will definitely be making again.
Lindsay Moe says
I’m so glad you enjoyed them Carly! They are definitely a favorite of mine as well!
H R says
Hi,
I made these cookies but somehow they turned out a bit too dry. I was short on cocoa powder so I added a bit more flour. I still have half the batter in the fridge.
Any ideas how to use the remaining dough with a better result? Should I add a spoon of milk to the dough?
Lindsay Moe says
Yes, I would try adding a splash of milk to see if that helps. In the future, if short on cocoa powder, I would probably leave the rest of the ingredients as is rather than substituting flour. I hope they turn out well for you!
Joni Ferrier says
I love baking but don’t really like eating what I bake. This is one of the cookies I definitely eat!
I make this slightly smaller because they tend to spread too much. Maybe it’s because I don’t wait for the melted butter to cool down? Will try to do that next time. I’m too impatient!
Carla says
I love these and have made them over and over for my family and our guests. We usually have whole wheat flour, so they’re convenient but also SO GOOD! They stay soft and, unlike other cookies, taste as good (or better) after being saved in the refrigerator.
Himika says
Absolutely yummy and delicious! My son loved it. Thank you so much 😊
Rhea says
Cookies turned out great, they were super fudgey and tasty
JCO says
Love the recipe – mine were undercooked at 9 minutes though, so kept them in for an additional 2-3 minutes. Still came out soft and moist.