I used to sell cookies at the farmers' market; I know what it takes to make the perfect chocolate chip cookie. Now 15 years later, I'm certified in holistic nutrition and am a mom who really cares about what my kids are eating. I've recreated the recipe to be a chewy whole-wheat chocolate chip cookie that I feel good about giving my kids for snack time or school lunches!
When I started converting my baking into healthy recipes, one of the first things I did was swap out white flour for whole-wheat flour. In these chocolate chip cookies (just like my whole-wheat chocolate chip muffins), the whole-wheat flour brings a complex nutty flavour, bringing more fiber, which will support the balance of blood sugar levels and increase the minerals in these cookies.
These days, I've started milling my own wheat berries to have fresh whole-wheat flour on hand. If you want to know the details about this, or if you want to use a bag of whole-wheat flour from the store for whole-wheat cookies, I share everything you need to know in this blog post.
When I started to convert my baking to contain more whole food options, the first thing I did was swap the white flour for whole-wheat flour. I learned it didn't always work as a 1:1 swap.
You need to think about the taste that you are going for: Is it light and airy? What texture? What taste? What rise? Sometimes you need to do half white flour and half whole wheat to make the vision come to life. I had to learn that some whole-grain flours absorb more liquid than others!
This recipe is my tested version for what I believe makes these perfect whole-wheat chocolate chip cookies.
Jump to:
- Danika's nutrition note: why I use whole-wheat
- Ingredients for whole-wheat chocolate chip cookies
- What kind of flour can I use for whole-wheat chocolate chip cookies?
- My step-by-step photos from my kitchen
- Tips for the best-tasting whole-wheat cookies
- Other wholesome chocolate chip snacks to make
- Whole-Wheat Chocolate Chip Cookies
- Danika Vanderpyl, C.H.N
Danika's nutrition note: why I use whole-wheat
When I studied nutrition, I was shocked to learn how many vitamins and minerals are stripped from whole grains to make white flour. Then flour companies began adding synthetic vitamins back into their products because people were getting sick without the nutrients—this is how “enriched” white flour came to be.
Whole grains are packed with natural goodness—especially ancient grains. They give protein, vitamins, and minerals, and even support the immune system. Just by swapping white flour for whole grain flours, you can make a real difference in your family’s health. This includes red wheat, einkorn, spelt, kamut, and emmer.
For this whole-wheat chocolate chip cookie recipe, I tested it with freshly milled red fife. Other whole-grain flours may give different results.
Now, 15 years after I first experimented with whole-wheat flour on a hunch that it was better, I choose to use whole grains and mill my own flour for the best nutrition. I’m just getting started, but I’m excited to explore how to create delicious food using more traditional and ancient grains—and I’d love for you to come along with me.
If you want to learn more, I really loved this podcast episode from Farmhouse on Boone about whole grains.
Ingredients for whole-wheat chocolate chip cookies
- Butter: I tested this recipe with melted butter and found that the cookies became too crispy. When I switched to using soft butter (not melted), they came out buttery and delicious! If you need to soften your butter, place it in the microwave for 10-second increments until soft.
- Light brown sugar: I used light brown sugar to get the perfect coloring of a chocolate chip cookie. Dark brown sugar will work just as well; however, you will get a darker cookie and a slightly more caramel taste.
- Sugar: I like to use organic cane sugar for this recipe, or regular white sugar works too.
- Egg: I tested this recipe with an egg and one yolk (which is often claimed to get a better chewy cookie), but really found I could get a chewy texture with just one egg, and then I wouldn't have to figure out what to do with a random egg white afterwards!
- Vanilla: Always add vanilla! To be honest, I usually add a full tablespoon (instead of 2 teaspoons) because it's so delicious, but that can get costly!
- Whole-wheat flour: For this recipe, you can use regular whole-wheat flour or white, whole wheat flour. I have started to mill my own wheat, so I like to use fresh milled red fife - more on this below!
- Baking soda: ½ teaspoon of baking soda is all you need; it will make the cookies spread, rise, and brown. I recommend testing and confirming that you have fresh and active baking soda by placing a little in lemon juice or vinegar. If it fizzes and bubbles right away, it's good to go; if not, time to buy some fresh baking soda.
- Salt: I always add a little sea salt to all my baking as it brings out the flavor. My favorite salt that is high in minerals is Redmond Real Salt.
- Chocolate chips: You can use milk chocolate chips, dark chocolate chips, mini chocolate chips, or chocolate chunks in these whole wheat cookies - whatever my kiddos like the most, but I try to stick to dark chocolate for less sugar!
See recipe card below for quantities.
What kind of flour can I use for whole-wheat chocolate chip cookies?
For this recipe, I’ve tested it with store-bought, regular whole-wheat flour and with fresh-milled Red Fife wheat berries — both worked great.
If you want a less nutty/whole wheat tasting, dense cookie:
- Use whole-wheat pastry flour or white whole-wheat flour,
OR
- Use half whole-wheat flour and half white flour. This is a great option if you’re starting to switch your family to more whole grains, have picky eaters, or want the cookies to taste like a classic bakery chocolate chip cookie.
Notes on other whole-grain flours:
- Rye will give you a more cakey cookie. I recommend using half rye and half white flour.
- Einkorn will make cookies softer and denser.
For more information on whole grains and baking with them, I've found this article on baking with whole grains super helpful, as I've been learning myself.
My step-by-step photos from my kitchen
- In a mixer, cream together the soft butter and sugars. Do this for about 1 minute on medium speed until everything is well mixed.
3. Add in the egg and vanilla - mix for about 30 seconds more until well-combined.
4. Add the whole-wheat flour to the mixing bowl, then sprinkle the salt and baking soda evenly over the top so everything mixes uniformly.
5. Turn the mixer on for another 30 seconds to 1 minute. I like to add the chocolate chips now while the mixer is going. When a dough forms and the chocolate chips are evenly distributed through the cookie dough. Turn the mixer off.
6. Your mixed dough will look similar to the photo above. It will be thick and soft. If you have a 1.5 tablespoon cookie scoop, use this, or simply use a tablespoon to make cookie dough balls. Place them straight onto a cookie sheet, without pressing them down (no need to grease the pan).
7. Bake cookies at 375 Fahrenheit (190C) for about 12-14 minutes; they will look puffy, cracked, and not fully cooked. Take them out of the oven and let the cookies finish cooking on the cookie sheet for 8-10 minutes to get a soft, chewy texture.
Tips for the best-tasting whole-wheat cookies
- I've made a batch of cookies with old whole-wheat flour that had been sitting in the back of the pantry for a longggg time. All you could taste was gritty whole-wheat flour, so don't do it; don't use old, rancid whole-wheat flour!
- Use a scale for the flour! If you haven't used a scale for baking before, now is the time to get it out, I beg you! Flour can be complicated to measure because there are two streamlined methods: scoop and level into the measuring cup, or dip the measuring cup into the flour to grab a scoop, which results in a much more packed cup of flour! If you use a scale, you will get the same exact amount I have tested this recipe with!
- If you are milling your own grains, use them right away, as it will create a better texture and the nutritional content is higher (fresh milled flour can go rancid quickly, as it does not have stabilizers like all-purpose flour)
- A little hack so they all look pretty and have even chocolate chips is to press a few more chocolate chips into each cookie dough ball right on the top before putting them in the oven!
- To get the perfect circular cookie, when they come out of the oven and they are still warm, grab a cup that is the same size or slightly bigger than the cookie, then place it on top to surround the cookie and use a circular movement to shape the cookie into an even circle!
Other wholesome chocolate chip snacks to make
Next, try these whole-wheat chocolate chip muffins, my favorite olive oil chocolate chip almond cookies, and these fun cookie dough bars!
🍪Did you make these whole-wheat chocolate chip cookies? Would you take 30 seconds to give a star rating and review just below the recipe? That means a lot to me and helps the growth of Beside the Mountain healthy snack blog.
Whole-Wheat Chocolate Chip Cookies
Equipment
- 1 Mixer
Ingredients
- ¾ cup butter, softened (280 grams)
- 1 cup golden brown sugar
- ⅓ cup white sugar
- 1 egg
- 2 tablespoons vanilla
- 2 ½ cups whole wheat flour (280 grams)
- ½ teaspoon baking soda
- ½ teaspoon sea salt
- 1 cup chocolate chips
Instructions
- Preheat the oven to 375°F (190°C). Place the soft butter, brown sugar, and white sugar into a mixing bowl. Mix on medium speed for about 1 minute, until it looks creamy.
- Add the egg and vanilla and mix for another 30 seconds.
- Dump the whole-wheat flour on top, then sprinkle the baking soda and salt so they don’t just land in one spot. Mix on medium until mostly combined, then toss in the chocolate chips and keep the mixer running until you have a soft, thick dough.
- Scoop the dough into balls with a cookie scoop or tablespoon. Place them on an ungreased pan with space to spread — no need to press them down.
- Bake one pan at a time at 375°F (190°C) for 12–14 minutes, until the cookies are flat, cracked, and just starting to brown. They might look a little underdone (that’s good!). Let them sit on the pan outside the oven for 9–10 minutes to finish setting. If you’re using convection, bake at 325°F (165°C) for the same time, and you can do two pans at once.
Notes
Nutrition
Danika Vanderpyl, C.H.N
I create snack recipes with healthy ingredients that are mostly already in your kitchen. I'm certified in Holistic Nutrition and I care about giving my kids real food. Let me share my nutrient-dense easy snacks with you.
Leave a Reply