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Home » Recipes » Appetizers & Snacks

Healthy Chocolate Chip Muffins

By: Kathryn Doherty | Last Updated: Mar 3, 2025 | Published: Feb 9, 2018
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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!

Close up of a couple of healthy oatmeal chocolate chip muffins on a red serving plate with chocolate chips scattered around.


 

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 for another time.

It's always nice to have chocolate on hand, right?

(Check out some of our other favorite healthy muffins.)

Oatmeal chocolate chip muffins in a muffin tin after baking.

I take a double batch of these muffins to teacher breakfasts at my kids’ preschool and they are always gone so quickly!

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 seriously 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.

Soft, fluffy and big chocolate flavor in every bite. ❤️

OK, let's get baking!

(You can also check out my Google web story for this chocolate chip muffins recipe.)

A healthy chocolate chip muffin tilted on its side in a muffin tin.

Now, I’ve got some notes and substitutions coming up below on how to make chocolate chip muffins. Just tryin’ to be helpful.

If you want to jump on down to the recipe, simply scroll right on through the rest of the text. The recipe card is near the bottom of the page, above the comments section.

Ingredient Notes:

  • Oats: Old fashioned rolled oats are my go-to here, but you could substitute quick oats if that's what you have. 
  • Milk: I've used skim milk, 2% and soy milk for these muffins and all work great. Unsweetened almond milk should be fine, too.
  • Flour: I use white whole wheat flour, which is a little lighter in texture and taste than whole wheat flour, while still being a whole grain. You can substitute whole wheat flour or all-purpose flour if you prefer. Or use a combination of whole wheat and all-purpose flour.
  • Butter: 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 might scramble the egg.
  • Chocolate chips: I use regular semi-sweet chocolate chips, but you could also try these with dark chocolate chips if you'd like. The recipe calls for a full cup, and they are chock full, but you can reduce this to ½ cup or ¾ cup if you want.

And while I don't do this, because my kids would balk, I know several readers have made these and added in chopped walnuts. Sounds like a yummy mix-in! 

Healthy chocolate chip muffins on a red plate with chocolate chips scattered nearby.

OK, let's talk about making these work for some various dietary needs.

If you need these to be dairy free, use a milk substitute, such as soy milk, and then use oil or applesauce in place of the butter.

You'll also need to make sure to use dairy-free chocolate chips.

You can also make them vegan!

Substitute a flax egg for the egg, use a milk substitute, oil or applesauce in place of the butter and vegan chocolate chips.

Finally, let's talk about what to do with the leftovers. Because they keep great and it's so wonderful to have some of these chocolate chip muffins tucked away for a rainy day!

A hand holding a chocolate chip muffin in its paper wrapper.

How to store muffins:

– These muffins will keep, covered, at room temperature for 3-4 days. After that, you can move them to the refrigerator, where they will keep for another 2-3 days.

– You can also freeze the extras. Let the muffins cool completely. Place them in a freezer-safe ziptop bag (that’s labeled!) and freeze for up to 6 months.

– I like to wrap them individually in aluminum foil before putting them into the bag. It adds an extra layer of protection from freezer burn and ice accumulation.

– To thaw, just place one or more muffins in the refrigerator overnight. Serve cold from the fridge or warm in the microwave for about 15-20 seconds.

– You can also warm a muffin in the microwave straight from the freezer in a pinch. Be sure to unwrap it and remove the foil. Start with 45 seconds and add time (and possibly turn it upside down) as needed.

Alright, I think you are all set! If you do have other questions, as always, let me know in the comments below. I’m happy to help!

Oh, and if you love healthier treats like we do, check out this chocolate chip zucchini bread that's whole wheat and sooo yummy!

I hope you make your first batch of these healthy chocolate chip muffins today. You’ll be coming back for more soon, I just know it.

Enjoy!

XO,

Kathryn

Close up of chocolate chip muffins on a colorful red plate with chocolate chips scattered to the side.
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4.34 from 423 votes

Healthy 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.
Prep Time15 minutes mins
Cook Time15 minutes mins
Total Time30 minutes mins
Yield: 12 muffins

Ingredients

  • 1 cup oats, I use old-fashioned oats
  • 1 cup skim milk, or soy or whatever you have
  • 1 cup white whole wheat flour, see notes
  • 1 teaspoon baking soda
  • ¼ teaspoon salt
  • ½ teaspoon cinnamon
  • ⅓ cup brown sugar
  • 1 large egg
  • ¼ cup unsalted butter, softened (see notes)
  • 2 teaspoons vanilla extract
  • 1 cup semisweet chocolate chips

Instructions

  • Preheat oven to 350. Line a muffin tin with muffin liners and spray with cooking spray.
  • Combine oats and milk and let those soak while you prepare the rest of the recipe, to soften the oats.
  • In a large bowl, whisk together the egg and brown sugar until smooth and caramel colored.
  • Add vanilla and butter and whisk to combine. You may have small pieces of butter in the mixture, which is totally fine. (See notes.)
  • Add flour, oat-milk mixture, baking soda, salt and cinnamon. Stir until well combined but don’t over mix.
  • Fold in the chocolate chips.
  • Distribute the batter between the muffin tins - they will be about ⅔rds full.
  • Bake for 15-18 minutes, until a toothpick comes out clean.

Notes

Oats: Old fashioned rolled oats are my go-to here, but you could substitute quick oats if that's what you have. 
Milk: I've used skim milk, 2% and soy milk for these muffins and all work great. Unsweetened almond milk should be fine, too.
Flour: I use white whole wheat flour, which is a little lighter in texture and taste than whole wheat flour, while still being a whole grain. You can substitute whole wheat flour or all-purpose flour if you prefer. Or use a combination of whole wheat and all-purpose flour.
Butter: 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 might scramble the egg.
Chocolate chips: I use regular semi-sweet chocolate chips, but you could also try these with dark chocolate chips if you'd like. The recipe calls for a full cup, and they are chock full, but you can reduce this to ½ cup or ¾ cup if you want.
Walnuts: Feel free to add some chopped walnuts to this recipe if you love those, ⅓ to ½ cup. Toasting them lightly first will give them extra flavor.
Storage tips: These muffins will keep at room temperature in a covered container or ziploc bag for up to 4-5 days. You can keep the in the refrigerator for another 2-3 days after that. They also freeze great! I wrap individual muffins in aluminum foil and then pop them in a freezer-safe ziploc bag. Thaw overnight in the refrigerator or microwave them (remove the foil first!) for 45 seconds or so, until thawed and warmed through.

Video

Nutrition

Serving: 1muffin | Calories: 198kcal | Carbohydrates: 27g | Protein: 4g | Fat: 9g | Saturated Fat: 5g | Polyunsaturated Fat: 4g | Cholesterol: 26mg | Sodium: 168mg | Fiber: 3g | Sugar: 14g
Tried this recipe?Leave a comment below or follow me on Instagram @familyfoodonthetable and tag me in your photo!

Note: This post was slightly updated in February 2018, however most of the text remains the same as the original April 2015 post.

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Reader Interactions

Comments

  1. Lisa @ Chocolate Meets Strawberry

    January 23, 2016 at 5:39 pm

    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 😀

    Reply
    • Kathryn

      January 25, 2016 at 6:17 am

      I hope you love these muffins Lisa! They are a definite favorite around here - for any time of day 🙂

      Reply
  2. Carlee

    March 04, 2016 at 3:57 pm

    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!

    Reply
    • Kathryn

      March 04, 2016 at 5:00 pm

      We are serious muffin people too 🙂 Hope you and your little man enjoy these! They're one of our favorites!

      Reply
  3. Frugal Hausfrau

    March 04, 2016 at 5:14 pm

    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

    Reply
    • Kathryn

      March 05, 2016 at 7:31 pm

      Thanks Mollie! Hope you give these a try - we LOVE them!

      Reply
  4. Nicole @ The Professional Mom Project

    March 05, 2016 at 8:59 pm

    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

    Reply
    • Kathryn

      March 07, 2016 at 10:03 am

      Thanks Nicole! These are a much healthier take on chocolate chip muffins and every bit as delicious!

      Reply
  5. Lou

    February 01, 2017 at 1:39 pm

    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.

    Reply
    • Kathryn

      February 01, 2017 at 8:28 pm

      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 (https://www.familyfoodonthetable.com/healthy-granola-muffins/) or my banana blueberry muffins (https://www.familyfoodonthetable.com/banana-blueberry-muffins/). 😊

      Reply
      • Shannon

        May 29, 2018 at 7:58 am

        Could you use honey instead of the sugar in this recipe?

        Reply
        • Kathryn

          May 29, 2018 at 10:22 am

          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

          Reply
    • Petra

      October 28, 2018 at 3:38 am

      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!

      Reply
      • Kathryn

        October 29, 2018 at 8:59 am

        I hope you enjoy them Petra!

        Reply
      • Muffinlover

        September 29, 2019 at 7:20 pm

        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

        Reply
        • Kathryn Doherty

          September 30, 2019 at 4:38 pm

          Yay! So happy to hear you love them! 😊

          Reply
  6. Christina

    February 06, 2017 at 8:08 pm

    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?

    Reply
    • Kathryn

      February 06, 2017 at 9:44 pm

      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!

      Reply
      • Christina

        February 08, 2017 at 6:42 am

        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!

        Reply
        • Kathryn

          February 08, 2017 at 9:50 am

          Oh great, so glad to hear that Christina - thanks for letting me know! Enjoy! 😊

          Reply
  7. Samantha

    February 10, 2017 at 10:48 am

    These look so good, making them as we speak! One question though. Is the mixture suppose to be so runny???

    Reply
    • Kathryn

      February 10, 2017 at 10:56 am

      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!)

      Reply
  8. Leona

    March 14, 2017 at 2:45 pm

    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!:)

    Reply
    • Kathryn

      March 14, 2017 at 9:45 pm

      I'm so glad to hear you loved these muffins Leona! They are a favorite around here!

      Reply
  9. Winnie

    February 10, 2018 at 1:04 am

    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!

    Reply
    • Kathryn

      February 11, 2018 at 6:41 am

      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!

      Reply
  10. Carmen

    March 05, 2018 at 11:47 am

    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!!!

    Reply
    • Kathryn

      March 05, 2018 at 4:08 pm

      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 😊

      Reply
  11. Gen

    April 28, 2018 at 9:15 am

    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.

    Reply
    • Kathryn

      April 29, 2018 at 3:38 pm

      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! 😊

      Reply
  12. An

    April 29, 2018 at 3:39 pm

    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?

    Reply
  13. An

    April 29, 2018 at 3:41 pm

    O and I used 1 cup of buttermilk instead of regular milk.
    Maybe too many adjustments. ...

    Reply
  14. An

    April 29, 2018 at 4:00 pm

    Sorry last thing. I used coconut sugar instead of brown sugar.

    Reply
    • Kathryn

      April 30, 2018 at 7:12 pm

      Hi, that is definitely lots of adjustments to the original recipe so it's hard to trouble shoot what might have been the problem.

      Reply
  15. Kelly

    May 18, 2018 at 9:41 pm

    Can I use this recipe to make mini muffins?

    Reply
    • Kathryn

      May 20, 2018 at 12:59 pm

      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!

      Reply
  16. Danielle

    May 23, 2018 at 7:46 am

    I made these but did mini muffins. I baked them for 12 minutes and they came great. I hope the kids love them!!

    Reply
    • Kathryn

      May 23, 2018 at 3:06 pm

      So happy to hear that they worked Danielle! I hope they love them too! 😊

      Reply
  17. Perdisha

    August 11, 2018 at 9:15 am

    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!

    Reply
    • Kathryn

      August 13, 2018 at 10:11 am

      Yay, I'm so happy you enjoyed them! Love that you added blueberries as well!

      Reply
  18. Jody Hand

    October 22, 2018 at 3:03 pm

    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

    Reply
    • Kathryn

      October 23, 2018 at 8:16 pm

      Oh I'm so happy to hear you all enjoyed these Jody! Thanks so much for sharing! 😊

      Reply
  19. Santini

    February 17, 2019 at 9:57 pm

    Looks so delicious! Can't wait to try this out! My kid's definitely going to love this! Thank you so much for sharing!

    Reply
    • Kathryn

      February 18, 2019 at 3:13 pm

      Thanks! I hope they do love them - my kids just finished off our latest batch. They can't get enough!

      Reply
  20. Dana Boynton

    March 01, 2019 at 3:17 pm

    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!!

    Reply
    • Kathryn

      March 04, 2019 at 3:59 pm

      Yay, I'm so happy you loved these Dana! Thanks so much for sharing! 😊

      Reply
  21. Elizabeth

    March 13, 2019 at 2:04 pm

    can you substitute buttermilk for milk?

    Reply
    • Kathryn

      March 13, 2019 at 5:54 pm

      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!

      Reply
  22. Ala’a

    March 31, 2019 at 6:18 am

    Hello there,

    Made it and turned out amazing, even my little kid loved it.. Added to recipe binder 😊

    Reply
    • Kathryn

      April 01, 2019 at 9:20 am

      I'm so happy you loved these! Thanks so much for sharing! 😊

      Reply
  23. Molly

    April 13, 2019 at 11:49 am

    If I don’t have brown sugar can I use regular white sugar? Thanks!

    Reply
    • Kathryn

      April 14, 2019 at 4:05 pm

      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!

      Reply
  24. Teah N.

    April 30, 2019 at 3:47 pm

    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.

    Reply
    • Kathryn

      May 01, 2019 at 12:06 pm

      I'm so happy to hear you both enjoyed them Teah! Thanks so much for sharing! 😊

      Reply
  25. Emily

    May 23, 2019 at 3:20 am

    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!

    Reply
    • Kathryn

      May 25, 2019 at 9:26 am

      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! 😊

      Reply
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Meet Kathryn

Hi there! I’m Kathryn Doherty, a cookbook author, mom of two, and devoted food and home cooking nut. I’ve got lots of easy recipes to help you get delicious food on the table for your family!

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