These healthy chocolate chip cookies take the classic recipe and make small tweaks for irresistible healthy cookies that are crispy on the outside, soft and chewy on the inside, and still sweet enough for a treat.

I don’t ever want to give up eating cookies.
But I have this thing with cookies, where anytime I make them, I eat them and then eat MORE of them. I love them so much, I have a hard time stopping at just one!
That’s one reason I created recipes like Healthier Sugar Cookies, Peanut Butter Oatmeal Cookies, and Dark Chocolate Chunk Oatmeal Cookies.
Classic chocolate chip cookies have been a bit tougher to get just right, but I finally did it! My irresistible healthy chocolate chip cookies are just as good as the original recipe, without nearly as much guilt if I end up eating half the batch!
HEALTHY CHOCOLATE CHIP COOKIES
If you like cookies as much as I do, you’re going to LOVE this healthier cookie recipe. These healthy cookies are:
- Chewy cookies on the inside
- Crispy cookies on the outside
- Irresistible (yes, it’s worth saying again!)
- Made with whole grains instead of white flour
- Still every bit of chocolate-y flavor
- Low sugar with just enough sweetener
- Vegan-friendly
WHAT MAKES HEALTHY COOKIES?
I’ve gone through MANY “healthy” chocolate chip recipes in search of THE BEST healthy cookies recipe, but I’ve found many of them change the classic chocolate chip cookie so much that you’re ending up with a completely different cookie.
- Some use oat flour. Which means you’re making Healthy Oatmeal Chocolate Chip Cookies.
- Some recipes use milk. This is weird to me since milk also dials down the sweetness of a cookie… which seems counterintuitive.
- A few healthy chocolate chip cookies recipes use a teeny tiny amount of chocolate chips. They’re using 2 Tablespoons per 12 cookies, which comes out to TWO chocolate chips per cookie. Uh-uh. That ain’t happening here.
- And some use no sugar and are sugar-free. They use maple syrup, applesauce, or banana to sweeten, which is fine if you want an applesauce or banana cookie. But we want a CHOCOLATE CHIP cookie, right?
My goal here is to make healthy cookies with wholesome ingredients that are better for you AND still taste like yummy chocolate chip cookies.
Since my husband said these were the best cookies ever made in our marriage (repeatedly!), and my kids kept telling me how good they were and that they were “the best cookies ever!” I’m pretty sure I’ve accomplished my goal!

HEALTHY CHOCOLATE CHIP COOKIE RECIPE INGREDIENTS
I grew up on the recipe on the bag of Nestle chocolate chips, so I know how good those are. But I also know how overloaded with sugar they are!
I’ve made some changes to that classic recipe that I think make the perfect, absolute best healthy chocolate chip cookies! Here’s what you need:
- Butter, softened. Required for chocolate chip cookies. Do not use melted coconut oil as a substitute – the cookies will spread and not rise.
- Coconut Sugar. It’s less processed than white sugar, contributing to the “healthier” aspect of the recipe. This is the brand I use. You can also use another granulated sugar, like turbinado sugar. The cookies will be darker in color if you use coconut sugar, and lighter with white granulated sugar.
- Egg. If you want a more cakey cookie, use just the egg yolk. Use the whole egg if you prefer a chewy texture and a soft cookie (with a bit more protein).
- Pure Vanilla Extract. Here’s how to make your own.
- Whole Wheat Flour. I like to use whole grain einkorn flour. You can substitute all-purpose flour or white whole wheat for whole wheat flour.
- Cornstarch + Baking Soda + Sea Salt. The corn starch gives the cookies that perfect chewy texture in the middle.
- Cinnamon. You can’t taste the cinnamon – I promise! Cinnamon tricks your taste buds into thinking the cookie is sweeter than it actually is.
- Dark Chocolate Chips. Dark chocolate chips have less sugar than semi-sweet or milk chocolate chips.
Like the regular recipe, but just a little bit different, right? We’re not doing anything crazy here, just minor tweaks for homemade chocolate chip cookies that are healthy, and no one will know the difference!
HOW TO MAKE PERFECT HEALTHY CHOCOLATE CHIP COOKIES RECIPE
If you start with the right ingredients, making the perfect chocolate chip cookie isn’t that hard. In fact, you’re probably familiar with these instructions:
Step 1. Cream the butter and sugar. In a bowl of a stand mixer, or in a large mixing bowl using a hand-held mixer, cream the butter and sugar together for one full minute. You want the butter to be light and fluffy and super creamy. (The color of the butter will ultimately depend on the type of sugar you use.)
Step 2. Add the wet ingredients. Scrape down the sides and mix in the egg and vanilla extract until they’re both combined.
Step 3. Add the dry ingredients. Scrape down the sides and add the flour, cornstarch, baking soda, sea salt, and cinnamon, and stir JUST until combined.
Tip: Sift in the flour for an even, soft-textured cookie. Don’t over-mix the dry ingredients! Otherwise, you’ll activate the gluten in the flour and make the cookie cake-like and chewy.
Step 4. Fold in the chocolate chips gently without overmixing. Don’t over-stir!
Step 5. Chill the dough. This step is mandatory, but I promise it’s worth it! Set the timer for 30 minutes and clean up the kitchen while you wait. Chilling the cookies solidifies the butter, giving you a cookie that won’t spread during the baking process.
Step 6. Preheat the oven to 350F.
Step 7. Measure the cookie dough. I like to use cookie scoops to ensure every cookie is the same size. Bake for 12 minutes. They will look slightly underbaked but will set as they cool. Cool the cookies on the baking sheet for 5 minutes before moving them to a cooling rack to cool completely.

VEGAN HEALTHY CHOCOLATE CHIP COOKIES
- Swap solid coconut oil for butter. Use one less tablespoon of coconut oil than butter. Make sure your coconut oil is not melted. You’ll also need additional chilling time to avoid the cookies spreading too much.
- Use a flaxseed egg instead of the egg. Here’s how to make a flaxseed egg.
- Swap chocolate chips for vegan chocolate chips. A great vegan-friendly brand to use is Enjoy Life. I get them here.
Note: You MUST refrigerate the vegan chocolate chip cookie dough for 2 hours before baking; otherwise, the room-temperature cookies will not set properly. You can also refrigerate overnight and bake the next day.

HOW TO FREEZE AND STORE HEALTHY CHOCOLATE CHIP COOKIES
To store baked cookies:
- For chewy chocolate chip cookies, store the baked cookies in an airtight PLASTIC container.
- For crispy chocolate chip cookies, store the baked cookies in an airtight GLASS container.
To freeze baked cookies:
- Let cookies cool completely on a cooling rack.
- Lay cookies flat on a baking sheet lined with parchment paper.
- Freeze for 2-4 hours, until thoroughly frozen.
- Remove from the baking sheet and store in a freezer-safe bag.
To freeze cookie dough:
- Before baking, scoop dough balls onto a baking sheet lined with parchment paper.
- Freeze for 2-4 hours, until thoroughly frozen.
- Remove from the baking sheet and store in a freezer-safe bag or container.
- Thaw cookie dough overnight in the fridge before baking as noted in the recipe.
- You can also bake directly from frozen by adding a few extra minutes to the bake time.

BABY STEPS FOR HEALTHY CHOCOLATE CHIP COOKIES
I didn’t do anything too wild with these healthy chocolate chip cookies – just small tweaks to make them better.
That same idea can apply to a lot of the food that you eat! Small changes can help you make better choices when it comes to all of your favorites.
- Lower the sugar. Whenever you make a sweet treat, chances are you can lower the sugar some without affecting the recipe.
- Use whole grains. Whether that’s switching flours, swapping brown rice for white rice, or using whole wheat pasta, eating the whole grain gives you more fiber, more vitamins and minerals, and helps keep your blood sugar stable.
- Keep it simple. Use real food ingredients and skip the added sweeteners, preservatives, and additives that come with processed foods.

CHOCOLATE CHIP COOKIES HEALTHY FAQS
Are homemade chocolate chip cookies healthy?
If you’re making the recipe on the bag of chocolate chips, not exactly. However, there are LOTS of ways you can make them more nutritious, including choosing better ingredients and using less sugar. I think you’ll find that this recipe is a perfect blend of both goals!
Which is better for cookies, butter or oil?
Butter is best for this healthy chocolate chip cookie recipe. It helps the cookies spread less and rise more. Either way, you’ll want to chill the dough before baking.
Are oatmeal chocolate chip cookies healthier than regular ones?
Oatmeal chocolate chip cookies are made with oats, which have more fiber than flour, and fiber makes you feel full. My Chocolate Chip Oatmeal Cookies are absolutely delicious, but they do have more sugar than this healthy chocolate chip cookies recipe.
Can you make these low sugar chocolate chip cookies?
Guess what – they already are! My recipe is truly low sugar – just ⅓ cup for a dozen cookies – the least amount of sugar that I found for any other low sugar chocolate chip cookies recipe.
How do you keep chocolate chip cookies soft?
There are several factors that come into play to keep chocolate chip cookies soft.
• Start with a good recipe.
• Don’t over-mix the cookie dough.
• Refrigerate the dough.
• Add one extra egg yolk (but not the whole egg) if you double the recipe below.
• Add cornstarch.
• Use brown sugar, which has molasses (or follow my tutorial to make brown sugar).
MORE HEALTHY SWEETS RECIPES
- Pumpkin Chocolate Chip Cookies
- Peanut Butter Chocolate Chip Cookies
- Healthier Candy Cane Cookies
- Pumpkin Cookies with Naturally Sweetened Cream Cheese Frosting
- Almond Thumbprint Cookies
- Snickerdoodle Cookies
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Healthy Chocolate Chip Cookies
These healthy chocolate chip cookies take the classic recipe and make small tweaks for irresistible healthy cookies that are crispy on the outside, soft and chewy on the inside, and still sweet enough for a treat.
- Prep Time: 10 minutes
- Cook Time: 12 minutes
- Total Time: 22 minutes
- Yield: 13 cookies 1x
- Category: Dessert
- Method: Bake
- Cuisine: American
Ingredients
- 6 Tbsp butter (84g)
- ⅓ cup coconut sugar (or other granulated sugar) (53g)
- 1 egg (50g)
- 1 tsp vanilla (4g)
- 1 cup + 2 Tbsp whole wheat flour (I use whole grain einkorn) (135g)
- 1 tsp cornstarch (2g)
- ½ tsp baking soda (3g)
- ¼ tsp salt (1g)
- ⅓ cup + 1 Tbsp dark chocolate chips (64g)
- ⅛ tsp cinnamon
Instructions
- Cream the butter and sugar. In a bowl of a stand mixer, or in a large mixing bowl using a hand-held mixer, cream the butter and sugar together for one full minute. You want the butter to be light and fluffy and super creamy. (The color of the butter will ultimately depend on the type of sugar you use.)
- Add the wet ingredients. Scrape down the sides and mix in the egg and vanilla extract until they’re both combined.
- Add the dry ingredients. Scrape down the sides and add the flour, cornstarch, baking soda, sea salt, and cinnamon and stir JUST until combined.
Tip: Sift in the flour for an even, soft textured cookie. Also don’t over-stir the dry ingredients, otherwise you’ll activate the gluten in the flour and make the cookie cake-like and chewy. - Fold in the chocolate chips. Don’t over-stir.
- Chill the dough. This step is mandatory, but I promise it’s worth it! Set the timer for 30 minutes and clean up the kitchen while you wait. Chilling the cookies solidifies the butter, giving you a cookie that won’t spread during the baking process. Preheat the oven to 350F.
- Measure the cookie dough and bake in the oven for 12 minutes. I like to use cookie scoops to ensure every cookie is the same size. Be sure to let them cool on the baking sheet for 5 minutes before moving them to a cooling rack to cool completely.
Notes
Vegan-Friendly Option
- Swap solid coconut oil for butter. Use one less tablespoon of coconut oil than butter. Make sure your coconut oil is not melted.
- Swap flaxseed eggs for the egg. Here’s how to make a flaxseed egg.
- Swap chocolate chips for vegan chocolate chips. A great vegan-friendly brand to use is Enjoy Life. I get them here.
Note: You MUST refrigerate the vegan chocolate chip cookie dough for 2 hours before baking, otherwise the room-temperature cookies will not set properly. You can also refrigerate overnight and bake the next day.






Can I use gluten free flour like Bob Mills 1 to 1 flour instead of wheat flour?
Sharon, yes but it may change the texture.
So I have decided to make this recipe but at the end when I went to go bake them…there was not baking time. You have a cool time but nothing else so how long do you bake them for?
Hello Denise,
Sorry about that! The recipe has been updated. The cookies should bake in the oven for 12 minutes. Hope this helps! 🙂
I made these cookies and favor was really good. Can you tell me anything about the nutrition information? Thanks Jen D
Hi Jen,
We’re so glad you enjoyed the recipe! We don’t add full nutrition info to our recipe because there can be user variations that will cause differences in nutritional values. You are more than welcome to use a free online nutrition calculator based on the ingredients that you are using in the recipe. Hope this helps! 🙂
Hi Jeannie! The recipe calls for 6 Tbsp of butter… not sure why you’d use less? But I’d love for you to try the recipe again as-written and update your ranking! 🙂
I would like to know if i can use king author’s organic wheat flour instead of Einkorn flour
Love this recipe idea! I’m a choc chip cookie addict so I want to try this healthier version. Something I noticed – they aren’t vegan since they include butter and eggs (animal products). But I’m not vegan anyway so it doesn’t bother me! thanks again
Hi Mary! We actually have vegan substitutes (coconut oil for butter, minus 1 Tbsp and MUST refrigerate before baking, and flax egg for egg) but completely forgot to include these in the recipe. We’ll get that fixed ASAP. I hope you like these cookies!
Thank you, thank you, thank you! I have been looking for a cookie recipe like this for years! Everyone loved them and my hubby was surprised when I told him they were 100% whole wheat with low sugar, even coconut sugar. This recipe is a keeper! Thanks again!
You’re so very welcome, Janelle!
Just made these today, exactly according to the recipe (except they were in the oven before I noticed the “chill 30 minutes” part). Delicious! Even without chilling, they were not too runny or too dry. Thanks for a great recipe! I’m curious…what does the corn starch do? I’ve been cutting the sugar in my recipes for a long time (usually by 50%) and one problem I have is the cookies turning out dry sometimes. Does the cornstarch help with that? Also, this recipe made exactly 14 cookies for me. Since I have 4 children, in the future I will double or triple, but wanted to give it a try at first. I will definitely be making again!
I’m so glad you liked these, Andrea! The cornstarch is a trick I learned from Sally’s Baking Addiction. I believe it helps to keep the cookie chewy!
I would love to have your Bulletproof Tea Latte recipe please
I’m a little confused- you stated that these cookies are “vegan-friendly” but there are butter and eggs in the recipe. Is there another option to make this vegan? Vegans don’t eat any animal products whatsoever. Thanks!
Hi Karyn! We tested this with flax-egg and they were delicious! Coconut oil didn’t fare so well, so I’d use a vegan butter instead. 🙂
Could I leave out the cornstarch I don’t have any?!
You can, but the texture will be just slightly different.
Can you use arrowroot flour instead of cornstarch?
I haven’t tested it, but I think you could!