I really did not think we needed another healthy banana muffin recipe. Of course, that was before a ripe bunch of bananas collided with cabin-fever restlessness induced by a persistent weather system best described as “ick.” I needed stimulation yet had lost all motivation to venture far from my oven. The solution? A recipe adventure! Healthy Banana Chocolate Chip Muffins were the happy discovery. One bite convinced me: we’ve been in dire straits without them all along.

Moist healthy banana chocolate chip muffins with applesauce. Easy, vegan, and whole wheat, these simple muffins are perfect for healthy breakfasts! Clean eating and kid friendly.

OK, maybe not dire.

We do have these classic Healthy Banana Muffins, Banana Bran Muffins, these blender Banana Oatmeal Muffins, plus a colorful collection of banana breads ranging from simple Healthy Banana Bread to Paleo Banana Bread to Zucchini Banana Bread to keep us fueled.

Plus, these fudgy, chocolaty Heathy Chocolate Muffins.

And yet, despite all the current options, these Healthy Banana Chocolate Chip Muffins are special and deserve a recipe of their very own.

Healthy Banana Chocolate Chip Muffins. Make ahead for breakfasts and snacks!

About This Healthy Banana Chocolate Chip Muffins Recipe

Yes, yes we do need one more healthy banana muffin recipe! Here are a few ways these particular Healthy Banana Chocolate Muffins are worthy of your efforts:

  • Mega MOIST, courtesy of applesauce. In addition to the natural moistness of the mashed bananas, these Healthy Banana Chocolate Chip Muffins have applesauce. It makes the muffins ultra tender without the need for adding extra fat.
  • Naturally VEGAN, thanks to flaxseeds. When combined with water, nutrient-rich flaxseeds gel and bind the muffins, in the same way eggs do. You can find flaxseed meal at almost any regular grocery store or online here.
  • WHOLE WHEAT. Yes to all of the fiber. These muffins will keep you full and happy.
  • CHOCOLATE CHIPS. My mix-in of choice. You can swap walnuts, dried fruit, or blueberries or omit the chips entirely if chocolate is not your preferred muffin addition. I won’t understand, but I’ll be happy you are eating the healthy banana muffins of your dreams.
  • EASY does it. These moist healthy banana muffins come together in ONE BOWL, no mixer required.
Banana Chocolate Chip Muffins. Easy, vegan, and healthy!

For those looking to pack meals for the office or to send them along to school, these whole wheat banana chocolate chip muffins are highly lunchbox friendly. I’ve even taken them with me to the gym a few times if I’m running errands right afterwards and need a healthy snack to tide me over until my next full meal.

How to Store and Freeze Banana Muffins

  • To Store. I’ve made these healthy banana muffins with applesauce a few times now, and I find that while not mandatory, it’s best to store them in the refrigerator to extend their shelf life.
  • To Freeze. Wrap each muffin in plastic, then place all of them in a ziptop bag and freeze for up to 2 months. Let thaw at room temperature or rewarm gently in the microwave.
  • For additional storage tips, check out my post on How to Store Muffins and Other Quick Breads.
Healthy Banana Chocolate Chip Muffins. Easy, moist, and kid friendly!

No matter how many different recipes I try, simple-yet-sublime treats like these Healthy Banana Chocolate Chip Muffins are ones I never grow weary of baking or eating.

The effort here is minimal, yet the reward is considerable. Plus, any recipe that allows us to eat chocolate for breakfast and feel great about it I consider a delicious victory!

Recommended Tools to Make Healthy Banana Chocolate Chip Muffins

Moist healthy banana chocolate chip muffins with applesauce. Easy, vegan, and whole wheat, these simple muffins are perfect for healthy breakfasts! Clean eating and kid friendly.

Healthy Banana Chocolate Chip Muffins

4.91 from 32 votes
Moist healthy banana chocolate chip muffins with applesauce. Easy, vegan, and whole wheat, these simple muffins are perfect for healthy breakfasts!

Prep: 10 mins
Cook: 25 mins
Total: 35 mins

Servings: 12 muffins


  • 1 tablespoon flaxseed meal OR 1 large egg (if you do not need the muffins to be vegan)
  • 3 large overripe bananas about 11 ounces (1 1/2 cups mashed)
  • 1/3 cup unsweetened applesauce
  • 2 tablespoons canola oil or melted cooled coconut oil*
  • 1/3 cup coconut sugar or light brown sugar
  • 1/4 cup pure maple syrup
  • 1 teaspoon pure vanilla extract
  • 1 teaspoon baking soda
  • 1/4 teaspoon ground cinnamon
  • 1/4 teaspoon kosher salt
  • 1 1/2 cups white whole wheat flour
  • 1/2 cup dark chocolate chips mini or regular (I used mini; dairy free if you’d like the muffins to be vegan)


  • In a small bowl, stir the flaxseed meal together with 2 1/2 tablespoons water. Set aside for 5 minutes to thicken. (This creates a flax egg. If you are using a regular egg, you can skip this step and add the egg with the applesauce in Step 3.)
  • Place the rack in the center of your oven and preheat the oven to 350 degrees F. Lightly coat a standard 12-cup muffin tin with nonstick spray.
  • Mash the bananas in the bottom of a large bowl until mostly smooth. Double check to ensure you have the 1 1/2 cups called for in the recipe. Whisk in the flax egg (or regular egg if not using flax), then the applesauce and oil. Whisk in the coconut sugar, maple syrup, and vanilla. Sprinkle the baking soda, cinnamon, and salt over the top, then stir gently until combined. Gently stir in the flour until barely combined, then fold in the chocolate chips, reserving a few for sprinkling on top if desired.
  • Divide the mixture evenly among the muffin cups and sprinkle on any reserved chocolate chips. Bake for 22 to 26 minutes, until a toothpick inserted in the center of a muffin comes out clean and the tops spring back lightly when touched. Place the pan on a wire rack and let cool for 5 minutes. Gently remove the muffins from the pan and place them on a wire rack to finish cooling completely, or enjoy immediately.


  • *If using coconut oil, be sure all of the ingredients are at room temperature and the coconut oil has cooled, or it will resolidify when it mixes with the cold ingredients.
  • I haven’t yet experimented with making these muffins gluten free. If you’d like to try, I would recommend starting with a 1:1 baking blend like this one.
  • Store muffins in the refrigerator for up to 5 days or at room temperature for 3 days, according to this guide for How to Store Muffins.


Serving: 1muffinCalories: 183kcalCarbohydrates: 32gProtein: 2gFat: 6gSaturated Fat: 2gFiber: 3gSugar: 18g

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Erin Clarke

Hi, I'm Erin Clarke, and I'm fearlessly dedicated to making healthy food that's affordable, easy-to-make, and best of all DELISH. I'm the author and recipe developer here at wellplated.com and of The Well Plated Cookbook. I adore both sweets and veggies, and I am on a mission to save you time and dishes. WELCOME!

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  1. Looks delicious! Loved watching your video! You look GREAT! Wow, a “flax egg.” I’m with you about the coconut sugar and maple syrup AND the chocolate! Thanks for another great recipe, and a perfect one for another snow day, Erin!

  2. It’s a yucky snowy day in Washington, DC, but these warmed my heart and stomach!
    I did not have white whole wheat flour in the pantry, but can attest they are still great using regular whole wheat flour. I also used an egg, lacking flax seeds. And normal size semi-sweet chips – because that’s what I had. Love that you can use what is on hand and the recipe still works!
    They came together really quickly and baked up beautifully.
    Thanks Erin!4 stars

  3. Hello! I love the idea of this recipe but I’m allergic to flaxseed and my son is allergic to eggs… could you recommend a substitute please? Chia?

    1. Hi Amy! Are there any other egg replacers you have had success with? I haven’t experimented with anything else in this recipe, so unfortunately I can’t say for certain.

      1. I regularly use a chia egg instead of flaxmeal with great success, they are pretty much interchangeable, I’m sure it’ll be fine.  Thanks for the video Erin I find them really helpful and entertaining. 

    1. Rya, I think you could play around with baking it in an 8×4-inch loaf pan. I’ve never tried but think it’s worth experimenting. Line the pan with parchment paper and coat it with nonstick spray. Bake for 50 to 60 minutes, until a thin knife inserted in the center comes out clean. To be safe, check at the 35-minute mark and tent the pan with foil if the bread is browning too quickly at the corners. If you decide to bake it this way, I’d love to hear how it goes!

  4. Hi! So I made this into a loaf and it was wonderful! I did as you said and I used whole wheat flour and honey instead of syrup. I also used a 9×5 loaf pan :) 
    Thanks for all your help! 5 stars

  5. Yum. Yum. I just made this recipe and you were right. They are moist and sweet. I am pregnant so I was able to eat 4 muffins without any guilt :) Thank you again for another recipe winner.5 stars

  6. Thank you for the suggestions inside your article. This helped with pantry-driven substitutions. These were delicious and husband approved to make again. They were so sweet and moist. 5 stars

  7. These are great! Light, fluffy and delicious. I wouldn’t change a thing and will make them often. Thanks for the recipe!5 stars

  8. Just popped a muffin tin of these in the oven. This is the second time I made these Healthy Banana Chocolate Chip muffins. They are moist, sweet and delicious — they taste sinful, but aren’t. I know they are healthy, but hard to believe. It is so unusual that a healthy muffin taste so good. They are wonderful.5 stars

  9. My 10 year old wanted to make muffins, and we wanted to make something that was tasty and had some nutritional benefits. These hit all the marks!
    We did sub out coconut oil for the canola oil, and used muffin liners. And I did 1/8 cup maple syrup and 1/8 cup dark molasses for the liquid sugar. And switched up the flour mixture to 1/2 cup almond flour, and 1 cup whole wheat flour.
    Baked for 26 minutes and they were perfect…and so good warm out of the oven, and clean up was so simple, as it was just the one bowl.
    I appreciate the tips on how to store them. I let them cool in the pan completely, then refrigerated in a sealed container for storage.
    Will definitely make these again!5 stars

  10. I just made these and followed recipe to the dot. They are absolutely splendid! I think these are the best banana muffins I’ve ever made. Thank you Erin! 5 stars

  11. I had all of the ingredients aside from whole wheat flour so I used Bob’s oat flour and they turned out great! I only used two bananas- I was unsure if I need them mashed in the measuring cup or just put in as pieces. Yummy recipe and so much healthier than store bought. Thank you!5 stars

  12. These are amazing and incredibly easy! I made them twice in the past two weeks they were THAT good!5 stars

  13. I was out of bananas and had applesauce on hand, so I thought I’d try these. Glad I did! They turned out moist and delicious. They disappeared just as fast as when I make the Healthy Banana Nut Muffins! Thanks for another healthy muffin recipe! Next, I want to try one with blueberries!5 stars

    1. I’m so happy that you enjoyed the muffins, Nena! Thank you for sharing this kind review!

  14. Found this recipe in a pinch and the muffins turned out sooo good and perfect! They were super easy to make & even my picky husband loved them. Yum, thank you!5 stars

  15. We make these muffins AT LEAST once a week. While we use egg instead of flax, I consider these to be a perfect recipe: easy to follow, easy to mix in one bowl, quick from start to finish, and unbelievably delicious for breakfast, snack, or dessert!5 stars

  16. Hi there ! Looking forward to trying this recipe! I don’t have whole wheat flour on hand but have almond flour – wondering if I could substitute ? Thanks in advance !

    1. Hi Emily! Since almond flour and regular flour react very differently in baking, I wouldn’t recommend this swap. However, you could use it in one of my almond flour recipes. I hope this helps!

  17. This is my favourite chocolate chip banana muffin ever. It’s so easy and quick. I didn’t have white whole flour so I just used simple whole wheat flour and turned out great. It’s super fluffy, you can taste the banana and it’s delicious. I left in in the oven for 30 mins cause my oven is a bit weaker.5 stars

  18. I’ve raved about this recipe in the past– back again. A favorite It is definitely my favorite p sweet tooth recipe without much guilt. I tripled it recently and froze most of the muffins so we could remove a few from the freezer at a time. Worked splendidly. I put 3-4 muffins in a small ziploc bag then put as many of the small ziplocks that fit into a freezer safe plastic container. The muffins, after thawing, taste fresh baked. That cannot be said of all recipes. These are yummy. My family loves them too!5 stars

  19. Omg Erin these are DE.LISH.IOUS!!!!!!! Super Moist. I added coconut flakes and a bit of honey to replace some of the maple syrup because maple syrup is expensive in canada! Thanks! Will be saving recipe for when I have kids. Should be soon ;)5 stars

  20. SO good. I used 2 cups mashed banana and used regular whole wheat flour (not white) only because that is all I had, and they turned out perfect. I will have to make a double batch next time as they went fast. This is my new go-to recipe for banana muffins. Thank you!5 stars

  21. I have made these so many times and they are delicious! I used less sugar and they are still sweet and satisfying!5 stars

  22. Great recipe! I even used a brown sugar alternative (swerve brown sugar replacement) and sugar free chocolate chips and these tasted just as delicious as a full sugar recipe, if not better!5 stars

  23. Making these again. This is one of the best muffin recipes ever.

    I usually double the recipe following it exactly, except for for two modifications. I use two large eggs when I double it and and, confess to adding extra (dark) chocolate chips.

    Our son made the recipe wants and added cocoa once to the recipe to make the muffins chocolate and they were delicious.

    This recipe freezes perfectly.
    Cindy5 stars

    1. I’m so happy that you’ve enjoyed the muffins, Cindy! Thank you for sharing this kind review!

  24. THIS RECIPE IS AMAZING! I have made it twice now and people are surprised there is no dairy or refined sugar in them.5 stars

  25. Suuuuper moist; so moist I might leave out the coconut oil the next time. They were a little too sweet for me and I may also try cutting back the sugar a bit. Other than that they are really good!4 stars

  26. I absolutely love this recipe. I have made it so many times – they are the most moist and delicious banana muffins I have ever made and my absolute favourite, hands down (and I’ve tried a lot of recipes of the years). Thank you for the recipe!5 stars