Healthy Banana Chocolate Chip Muffins are moist, soft, and ready in 30 minutes. Packed with protein and potassium, yet without refined sugars, they deliver enough sweetness that kids still consider them a treat!

Don’t let the rest of your ripe bananas go to waste! Keep them for banana protein muffins and almond flour banana muffins.

Healthy banana chocolate chip muffins in paper liners and banana nearby.

These healthy banana chocolate chip muffins contain so many nutritional benefits while giving us a soft and moist bakery style muffin.

We’re using ripe bananas which deliver sweetness and moisture, Greek yogurt for protein, a hint of cinnamon for added flavor, and loads of chocolate chips! Banana chocolate chip muffins are a delicious cross of my healthy banana muffins and healthy chocolate chip muffins.

Take these healthy muffins on the go as a healthy snack or pack one in your lunchbox. Enjoy it on its own or slathered in melted butter!

Ingredients for Healthy Banana Chocolate Chip Muffins

To make healthy banana chocolate chip muffins recipe, you will need a few simple ingredients.

Spelt flour, bananas, yogurt, maple syrup, oil, dark chocolate chips, egg, baking powder, baking soda, salt, vanilla extract, cinnamon.
  • Bananas: You’ll need about 3 large bananas. The riper the bananas the better. Brown spots, brown patches, bruised, and scary-looking bananas are what we’re looking for! Frozen bananas are OK too.
  • Egg: Just one is all you need for binding the ingredients together.
  • Greek yogurt: I prefer to use 2% fat yogurt for moisture and richness. You can use 0% fat yogurt but muffins will be less moist.
  • Maple syrup: It has a delicious flavor that pairs well with cinnamon, vanilla, and chocolate chips. Honey or any other liquid sweetener works.
  • Oil: Olive oil, avocado oil, or melted coconut oil is neutral in flavor and contains healthy fats.
  • Whole wheat flour: Or spelt flour. You could also try white whole wheat flour or pastry wheat flour.
  • Baking staples: Cinnamon, baking powder, baking soda, salt and vanilla extract.
  • Chocolate chips: I use dark chocolate chips. You can swap them for any of your favorite chocolate chips.

How to Make Healthy Banana Chocolate Chip Muffins

These healthy banana chocolate chip muffins come together in one bowl.

  • Mash bananas and add liquid ingredients: In a large bowl, mash ripe bananas using a fork. Then, whisk together the egg, yogurt, maple syrup, oil, vanilla, cinnamon, baking powder, baking soda, and salt.
  • Make banana muffins batter: Add flour and gently stir the muffin batter. Make sure everything is incorporated without overmixing.
  • Let the batter rest: Just for a few minutes, so the flour has time to absorb into the rest of the ingredients and the leavening agents have time to start working towards light and fluffy muffins!
  • Fold in the chocolate chips and divide the batter: Add chocolate chips and give batter a few stirs. Use an ice cream scoop to scoop the batter and fill each opening of the prepared muffin tin to about 3/4 full. Place a few extra chocolate chips on top of the muffins.
  • Bake muffins: Bake banana chocolate chip muffins on the middle rack for 20 minutes. Muffins are ready when a toothpick inserted in the center comes out clean. Let the muffins cool for 5 minutes.

Tips for Best Results

Here are my top tips for best healthy banana chocolate chip muffins in the world!

  • Follow the recipe: It’s important with muffin recipes, to keep the ratio of liquid ingredients to dry ingredients as listed in the recipe. If you plan to swap sweeteners, make sure they’re liquid and not dry like granulated sugar.
  • Do not overmix the batter: This will activate the gluten and release too much of the trapped air leaving muffins heavy, dense, and rubbery.
  • Do not over bake: Remove banana muffins from the oven as soon as toothpick comes out clean to avoid dry muffins, even if they look not too browned. Muffins keep cooking with residual heat.
  • To ripen bananas fast: Place a few ripened apples or bananas with the unripened ones in a tightly sealed brown paper bag. Leave on the counter for a couple of days and allow the ethylene gases to speed up the process. If you’re in more of a hurry, bake the entire banana (peel and all) in an oven at 350 degrees for 15-20 minutes.
Healthy banana chocolate chip muffin with a bite taken out of.


Here are a few fun additions and swaps for your healthy banana chocolate chip muffins depending on your taste and what you have on hand.

  • Applesauce: You can replace the yogurt with sweetened applesauce or unsweetened applesauce, if desired.
  • Egg-free: Omit the egg and use a flax egg or chia egg in its place. Banana chocolate chip muffins will just rise less.
  • Add-ins: Use fresh blueberries or frozen blueberries instead of chocolate chips. Add some chopped walnuts, pecans or almonds for crunch. Add up to 1/3 cup of coconut flakes.
  • Make mini muffins: Use a mini muffin tray to make double the amount of smaller muffins. Bake for 15 minutes and test with a toothpick. Leave them in a little longer, if they need it.

How to Store Healthy Banana Chocolate Chip Muffins

To store: Keep healthy banana chocolate chip muffins moist covered in on your countertop for 2 days. You can then transfer them to the refrigerator for a few extra days.

To freeze: Bake, cool completely and transfer muffins to a freezer-friendly bag. Freeze for up to 3 months. To thaw, let muffins sit at room temperature on the counter for a few hours.

Storage Tip

For more tips and tricks to make your leftover muffins stay fresh longer, check out my posts how to store muffins and how to freeze muffins.


Can I make this banana muffin recipe with gluten free flour?

I haven’t tried it but if I were to, I would probably stick with a 1:1 all-purpose gluten-free flour. I do not recommend to use almond flour or coconut flour as it acts differently. Check my list of gluten free banana muffins recipes below and just add chocolate chips.

Can I make vegan banana chocolate chip muffins?

Yes. Swap the yogurt with a dairy free yogurt like coconut yogurt, and the egg with an egg replacer. Or try my vegan banana muffin recipe and add chocolate chips.

Do I have to refrigerate healthy banana chocolate chip muffins?

Healthy banana chocolate chip muffins can stay out at room temperature for a couple of days. After store in the fridge for 2-3 more days.

Can I make these muffins into banana chocolate chip bread?

You can. Bake bread at 350 F for 50-60 minutes. Use the toothpick method to check to see if it’s done.

Can I make these healthy banana chocolate chip muffins with all-purpose flour?

I think so but I haven’t tried. Use 1 cup of white flour for every 3/4 cup of whole wheat flour that recipe calls for.

More Banana Recipes to Try

More Banana Muffins to Try

Healthy banana chocolate chip muffins in a blue muffin tin.
healthy banana chocolate chip muffins

Healthy Banana Chocolate Chip Muffins

Healthy Banana Chocolate Chip Muffins are moist, soft, and ready in 30 minutes. No refined sugars, yet kids still consider them healthy treat.
4.72 from 14 votes
Servings 12 muffins
Calories 180
Prep Time 10 minutes
Cook Time 20 minutes
Total Time 30 minutes



  • Preheat oven to 375 degrees F, line 12 muffin tin with parchment paper liners and spray with cooking spray. Set aside.
  • In a large mixing bowl, add bananas and mash with a fork. Add the egg, yogurt, maple syrup, oil, vanilla extract, cinnamon, baking powder, baking soda and salt; whisk well to combine.
  • Add flour, gently stir until well incorporated but do not overmix. Let batter sit for a few minutes to absorb the flour, add chocolate chips and stir a few times.
  • Using an ice cream scoop, fill each opening of a muffin tin 3/4 full and add a few extra chocolate chips on top (optional). Bake on a middle rack for 20 minutes or until a toothpick inserted in the center comes out clean.
  • Let muffins cool for about 5 minutes and enjoy!


  • Store: Covered in a cool dry place for 2 days. Then refrigerate in an airtight container for another 3 days.
  • Freeze: Freeze for up to 3 months. To thaw just remove muffins from the freezer and let defrost for a few hours or overnight on a counter.
  • Bananas: Choose very ripe bananas that are yellow with many brown spots to brown patches. Bruised bananas are even better. Scary looking brown bananas are awesome.
  • Liquid sweetener: Not dry sweetener like sugar please. You have to keep dry to wet ingredients ratio.
  • Yogurt: You can use 0% yogurt, however muffins will be less moist. Regular (not Greek) yogurt will work as well, so will sweetened or unsweetened applesauce.
  • Other sizes: Bake mini banana muffins for 15 minutes and do a toothpick test. Bake longer, if necessary.


Serving: 1muffin | Calories: 180kcal | Carbohydrates: 28g | Protein: 4g | Fat: 7g | Saturated Fat: 3g | Trans Fat: 1g | Cholesterol: 14mg | Sodium: 147mg | Fiber: 3g | Sugar: 13g
Course: Muffins and Quick Bread
Cuisine: North American
Author: Olena Osipov
Did you make this recipe?Mention @ifoodreal or tag #ifoodreal!

5 Secrets to Easy Healthy Dinners

Plus sign up for weekly emails with recipes to make your cooking stress free, delicious and healthy.

About Olena

Welcome! I grew up in Ukraine watching my grandma cook with simple ingredients. I have spent the last 11 years making it my mission to help you cook quick and easy meals for your family!

Pin this recipe now to save it for later

Pin Recipe

You may also like


  1. 5 stars
    I made these diary chocolate chip banana muffins with 3% regular yogurt instead of the greek yogurt, substituted the melted coconut oil with melted butter and substituted the flour with gluten free Sorghum flour and they came out really moist and yummy. Thank you for this awesome recipe!!

  2. 5 stars
    Made this yesterday with my kids! AMAZING!!!!!! I doubled the batch and froze six for healthy school snacks. They were so good they barely made it that far!
    Thanks Olena. This recipe is a winner!!!

    1. Baking is a science and the recipe has not been tested as such, usually though you will just need to add more all purpose flour as wheat is more dense.

  3. 5 stars
    We have overripe bananas to use this weekend. I made this recipe and added blueberries since I did not have chocolate chips on hand. They are healthy and delicious- my son and husband loved them!

Leave a Reply

Your email address will not be published. Required fields are marked *

Recipe Rating

This site uses Akismet to reduce spam. Learn how your comment data is processed.