Healthy chocolate chip muffins are 100% whole grain, low in sugar and can be made dairy-free. They’re soft, fluffy and seriously loaded with chocolate chips. They’re great for a fun breakfast or lunchbox treat or an afternoon or late-night snack!
Note: This post was slightly updated in February 2018, however most of the text below remains the same as the original April 2015 post. I also added a new recipe video – check it out!
Can I just say, we love, love, love these muffins! ❤️
I’ve probably made 50 batches of these in the last few years. Maybe more.
These healthy chocolate chip muffins are on my list of foods to take to new moms because they are great for breakfast, snack, dessert and in the middle of the night when you’re feeding a newborn. Plus they freeze great so you can stash some away. 👍
It’s always nice to have chocolate on hand, right?
(Check out some of our other favorite healthy muffins.)


I take these muffins to the teacher breakfasts at my kids’ preschool because they’re healthy but also feel so indulgent. I make double batches and I’m sure it would be appreciated if I made a triple batch. Maybe next time around…
I make these chocolate chip oat muffins for my family on a regular basis, too, and my husband is always asking if we have any extra hiding somewhere in the freezer.
They don’t last long around here. Maybe I should make double batches for us, too. 😊

These whip up so quickly and come out perfect and delicious every time. I can’t resist them.
And knowing they are 100% whole grain, with just a small amount of butter and brown sugar, well, I’m completely happy not to resist. Just to give in.
Soft, fluffy and big chocolate flavor in every bite. 🍫❤️😍
Notes on healthy chocolate chip muffins:
- I’m lazy and usually melt my butter in the microwave. Who has time to let it soften? Just don’t add it to the egg while it’s super hot or you’ll scramble the egg.
- I’ve used skim milk, 2% and soy milk for these muffins and all work great. Unsweetened almond milk should be fine, too.
- If you need these to be dairy free, use a milk substitute, oil or applesauce in place of the butter and dairy-free chocolate chips.
- I use white whole wheat flour, but you can substitute whole wheat flour or all-purpose flour if you prefer.
- These freeze great! I wrap individual muffins in aluminum foil and then pop them in a freezer-safe Ziploc bag for up to 5 months.

Make your first batch of these healthy chocolate chip muffins today. You’ll be coming back for more soon.
Enjoy!
XO,
Kathryn
P.S. Don’t miss my video on how to make these chocolate chip muffins!
Healthy chocolate chip muffins are 100% whole grain, low in sugar and can be made dairy-free. They’re soft, fluffy and seriously loaded with chocolate chips. I use white whole wheat flour, but you can substitute whole wheat flour or all-purpose flour if you prefer. I'm lazy and usually melt my butter in the microwave, which is fine too. You can also sub 1/4 cup oil or 1/4 cup applesauce in place of the butter if you prefer. These freeze great! I wrap individual muffins in aluminum foil and then pop them in a freezer-safe Ziploc bag. Remove one at a time - or more - and microwave until warm, about 30 seconds. As an Amazon Associate and member of other affiliate programs, I earn from qualifying purchases.Healthy chocolate chip muffins

Ingredients
Instructions
Notes
Recommended Products
Nutrition Information:
Yield:
12 Serving Size:
1 muffin
Amount Per Serving: Calories: 212 Total Fat: 9g Saturated Fat: 5g Trans Fat: 0g Unsaturated Fat: 4g Cholesterol: 26mg Sodium: 168mg Carbohydrates: 28g Fiber: 3g Sugar: 15g Protein: 4g









Lisa @ Chocolate Meets Strawberry says
Going to make these ones soon! I made up a big batch of applesauce yesterday, as I love to always keep some on hand to eat with yoghurt or on top of my oats for breakfast, and I have some wholemeal spelt flour in the cupboard, so I can actually make these! With a new week of work just around the corner (minus a public holiday on Tuesday, hehe!), these will be great for work lunches 😀
Kathryn says
I hope you love these muffins Lisa! They are a definite favorite around here – for any time of day 🙂
Carlee says
My little guy and I love muffins. We haven’t made a batch in at least a couple of months though. These will have to break that dry spell! Thanks for sharing at Throwback Thursday!
Kathryn says
We are serious muffin people too 🙂 Hope you and your little man enjoy these! They’re one of our favorites!
Frugal Hausfrau says
Now these look fantastic!! If you could ever pry one of my muffins out of my hand, I’d eat one in a heartbeat! lol~ Seriously, we could use a healthier muffin recipe and I’m looking forward to trying it.
And as usual, lol, Thanks for sharing this with us on Throwback Thursday~
Mollie
Kathryn says
Thanks Mollie! Hope you give these a try – we LOVE them!
Nicole @ The Professional Mom Project says
These look delish! I love chocolate chip muffins but they are often so unhealthy I’ll have to try this recipe. Found your post at #ThrowbackThursday
Kathryn says
Thanks Nicole! These are a much healthier take on chocolate chip muffins and every bit as delicious!
Lou says
I’m sorry to say but there’s nothing “healthy” about these muffins. They’re still packed with sugar (just because it’s brown sugar doesn’t mean it’s healthy) and butter. I’m sure they’re delicious but they aren’t considered healthy.
Kathryn says
Hi Lou! Yes, they do still have butter and sugar, but these have MUCH less than other versions and they are completely whole grain. Also, while there’s only a teaspoon of butter in each muffin, you can substitute with oil or applesauce as noted above for an even lighter version.
You can also check out some of my other muffins and baked goods that are refined sugar-free and have no butter or oil – like my granola muffins (http://www.familyfoodonthetable.com/healthy-granola-muffins/) or my banana blueberry muffins (http://www.familyfoodonthetable.com/banana-blueberry-muffins/). 😊
Shannon says
Could you use honey instead of the sugar in this recipe?
Kathryn says
I haven’t tried that, so I’m not sure. You would need to adjust the amount of the honey as well as the amount of liquids in the recipe. Here’s a good article though with some tips: https://www.thekitchn.com/4-rules-for-successfully-swapping-honey-for-sugar-in-any-baked-goods-230156
Petra says
I agree, I often see recipes being called “healthy” when in fact they’re just not quite as unhealthy as most similar ones. But if we want healthy food, muffins is probably not what comes (or should come!) to mind anyway. I will give these a try today, fully knowing they’re just “not quite as unhealthy as regular muffins”. 🙂 They look yummy!
Kathryn says
I hope you enjoy them Petra!
Muffinlover says
I don’t get the point of even posting that. Like she said above, they are better than what you get at the store. Stay positive people!
Ps. I love these muffins
Kathryn Doherty says
Yay! So happy to hear you love them! 😊
Christina says
I just made these muffins today and they are delicious! The only problem we had is that they fell apart. I used oil and not butter. Any ideas as to what we could do to make the muffins stay together?
Kathryn says
Hi Christina! I’m so glad you enjoyed them but I’m sorry they fell apart. I’ve made these dozens and dozens of times and haven’t had that problem. (I almost always use butter or applesauce but the oil shouldn’t make that much of a difference.) My only advice would be to make sure the muffins are fully cooked in the oven and then to let them cool so they set all the way up. Hope that helps!
Christina says
Hi there!
I have an update. The next morning, the muffins were no longer falling apart!
We still love them so we are going to try again and bake them a little more.
Thanks!
Kathryn says
Oh great, so glad to hear that Christina – thanks for letting me know! Enjoy! 😊
Samantha says
These look so good, making them as we speak! One question though. Is the mixture suppose to be so runny???
Kathryn says
Yup, it is a pretty liquidy batter – the oats soak up a lot of the liquid as they cook. I hope you love them! (And I’m actually planning to make them on Facebook Live tomorrow if you want to check it out!)
Leona says
I used and or added instant Oates, almond milk, 2 mashed bananas and some chopped walnuts and just greased the muffin tin! Turned out moist and delish! Cooked them a bit longer and made 12 large muffins!:)
Kathryn says
I’m so glad to hear you loved these muffins Leona! They are a favorite around here!
Winnie says
These look so delicious. I will probably use a combination of all-purpose and whole wheal floor like I usually do in muffins so my kids like them. I wonder how soft the oats become. I’ll have to try the recipe. If there is too much texture my kiddos will probably not eat them. Anyway, that will mean more for me!
Kathryn says
Hi Winnie! That should be just fine to use a mix of flours. And the oats soften all the way so there hopefully isn’t a texture issue. (Though that might mean you have to share 😄) I hope you enjoy them!
Carmen says
I’m enjoying one of these muffins as I write, they are delicious!!!! I baked a double batch to freeze some for use later in the month. I used applesauce and white whole wheat flour; they came out moist, fluffy, chocolatey and with a bit of texture from the oats, something I really like. The only thing I will change next time is add less chocolate chips. Keep on bringing muffin’s recipes please!!!
Kathryn says
I’m so happy to hear you love them, Carmen! Thanks so much for sharing! And I will definitely keep bringing the muffin recipes – we can’t get enough! Here’s my collection of all of them if you want to check it out: https://www.familyfoodonthetable.com/category/muffins 😊
Gen says
I ended up making two batches , because I thought I’d screwed up the first since they were still raw at 15 minutes. It turns out I needed to cook them for 23 minutes instead. I also decreased the amount of chocolate chips to 2/3 cup, and it was still plenty.
Kathryn says
I’m so happy you enjoyed them and figured out you needed a little longer baking time! And yes, the full recipe with 1 cup of chocolate chips is REALLY loaded! 😊
An says
Just made these. Although they taste really great I made some adjustments. I used less chocolate chips and used 2 cups of oatmeal instead of 1 cup oatmeal and 1 cup wholemeal flour… i thought to make it healthier this way. Also used virgin coconut oil instead of butter. But …it took about 37 minutes to bake. Even after 25 minutes the inside was still very moist. The muffins didn’t really rise, is it the way it should be? I also first grinded the oats so they’d be having a flour texture. Now they’re cooled off and just had one. My husband likes it but I find they are a bit heavy to swallow. Maybe I should have added that 1 cup of wholemeal flour instead of putting 2 cups of oats?
An says
O and I used 1 cup of buttermilk instead of regular milk.
Maybe too many adjustments. …
An says
Sorry last thing. I used coconut sugar instead of brown sugar.
Kathryn says
Hi, that is definitely lots of adjustments to the original recipe so it’s hard to trouble shoot what might have been the problem.
Kelly says
Can I use this recipe to make mini muffins?
Kathryn says
I haven’t tried that but I’m sure you could! It would probably be 10-13 minutes for the baking time, and you might want to use mini chocolate chips instead. Would love to hear if you make them!
Danielle says
I made these but did mini muffins. I baked them for 12 minutes and they came great. I hope the kids love them!!
Kathryn says
So happy to hear that they worked Danielle! I hope they love them too! 😊
Perdisha says
I just made these (used oil instead of butter as suggested) and added blueberries with the chocolate chip the result is amazing ! The muffins themselves are moist and delicious, will be making these again!
Kathryn says
Yay, I’m so happy you enjoyed them! Love that you added blueberries as well!
Jody Hand says
YUMMMMMM!! My kids loved this healthier alternative muffins. Thank you so much for the great recipe. And while I appreciate they are not HEALTHY to the letter, they are most certainly healthier than anything else I can find that my children actually ate and enjoyed. I used the applesauce instead of the butter and they were perfect. Good to note that the batter is super runny – glad to have read through the reviews so I didn’t think I screwed up too bad while making them LOL Thank you once again! Make it a great day 🙂 Jody
Kathryn says
Oh I’m so happy to hear you all enjoyed these Jody! Thanks so much for sharing! 😊
Santini says
Looks so delicious! Can’t wait to try this out! My kid’s definitely going to love this! Thank you so much for sharing!
Kathryn says
Thanks! I hope they do love them – my kids just finished off our latest batch. They can’t get enough!
Dana Boynton says
I just made a batch. I substituted apple sauce for butter. I absolutely love them! I even added more chocolate chips than the 1 cup, but will def put in less next time. So delicious thank you!!
Kathryn says
Yay, I’m so happy you loved these Dana! Thanks so much for sharing! 😊
Elizabeth says
can you substitute buttermilk for milk?
Kathryn says
Hi Elizabeth, I’m not sure, as I’ve never tried making them with buttermilk. It would likely change the chemistry of the muffins a bit so you may need to make other adjustments. Here’s a good article for reference: https://www.thespruceeats.com/buttermilk-substitutions-measures-and-equivalents-1807462 Hope that helps!
Ala’a says
Hello there,
Made it and turned out amazing, even my little kid loved it.. Added to recipe binder 😊
Kathryn says
I’m so happy you loved these! Thanks so much for sharing! 😊
Molly says
If I don’t have brown sugar can I use regular white sugar? Thanks!
Kathryn says
I haven’t made them that way and while it might alter the taste just a bit, I think it should be fine. Would love to hear if you try it!
Teah N. says
Hello I made these and they were so good! My daughter and I ate them while they were still warm and they were moist and the chocolate chips gave them just the right amount of sweetness.
Kathryn says
I’m so happy to hear you both enjoyed them Teah! Thanks so much for sharing! 😊
Emily says
Wow, I wish I had found these earlier! They are my new favourite healthy chocolate chip muffin recipe! So moist and delicious, aswell as keep fresh for so long!
Kathryn says
Yay, I’m so glad you love them Emily! They are our favorite too – my kids are begging me to make another batch this weekend! 😊
Dee says
This recipe turned out amazing! Delicious and great texture, call me impatient, but I ate one right out if the oven when they were done! I ran out of baking soda so I put a teaspoon of baking powder instead. I also redid the sugar to 1/4 cup and chocolate chips to 3/4 cup. This one is definitely a keeper.
Kathryn says
Oh I’m so happy to hear you loved them!! Thanks so much for sharing! 😊
Brittany says
These turned out great! I used 1/2 c white flour, 1/2 c whole wheat, coconut sugar in place of brown sugar, 2 Tb of applesauce + 2 Tb of coconut oil, and only 1/2 cup mini chocolate chips. With my substitutions I calculated it to be about 11 grams of added sugar per muffin. Will definitely make again!
Kathryn Doherty says
I’m so glad you enjoyed these Brittany! And thanks so much for sharing your subs – that’s really helpful! 😊
Amy says
Just made a second batch of these over the weekend, and I have to say, the recipe as it’s written is a good start, but needs some tweaks. I added more spices because it tasted like it was missing something. I added allspice, cloves and nutmeg, along with the cinnamon. I also doubled the recipe, because honestly, I eat 2 at a time for breakfast and a single batch/recipe goes fast. Another change I made was I didn’t soak the oats in the milk, instead, I mixed everything together and let it all soak together for at least 30 minutes. The last two things I changed, I used mini chocolate chips (since I used a cupcake pan, the regular sized chocolate chips seemed to be too much for the smaller sized muffins), and I added walnuts. Which after my first batch I realized I needed to toast them first.
I may bump up the amount of spices I add next time I make these, while the additional spices helped, I feel like I could double the amounts that I added, to give more flavor. The nutmeg was the one that stood out to me, which was freshly grated.
Kathryn Doherty says
Thanks for sharing your substitutions! Love the sound of those extra spices for the holiday season (though I’m not sure my kids would enjoy them as much that way)!
Amy says
You’re welcome! Honestly, the extra spices just add to the flavor. If you make sweet potatoes for the holidays, maybe give them a dusting with the spices I mentioned, get the family used to the flavors. That might help them get used to the flavors.
Adam says
Says baking soda in written instructions and baking powder in video?
Kathryn Doherty says
Yes, sorry about that, it should be baking soda, as in the written instructions. I hope you enjoy them!!