Healthy Chocolate Chip Banana Muffins

by Caroline
Published: Last Updated on

Made with whole wheat flour, greek yogurt, coconut oil, and reduced white sugar, you can feel good about eating these healthy chocolate chip banana muffins for breakfast. They are tender, sweet, and made with wholesome ingredients! 

If you can’t tell already, I love baking with bananas. I’ll often buy a bunch of bananas and purposely allow them to brown deeply on my counter just so I can bake with them. 

I could make banana bread every week. It’s a nostalgic recipe for me. 

What I love most about baking with bananas is the amount of moisture they bring to a recipe. While most banana bread and banana muffins call for a hearty amount of sugar and fat, it’s not really necessary. 

Let me tell you – my healthy banana muffins are so tender and moist, you won’t miss the extra sugar or oil. 

This recipe calls for chocolate chips, but you can use whatever mix-ins you have on hand to make your new favorite healthy banana muffin. 

Why You’ll Love Healthy Chocolate Chip Banana Muffins: 

  • They are Tender – The muffins are light and soft. You’ll notice the tender crumb at first bite. 
  • They are Moist – No dry muffins here! Bananas, yogurt, and just enough white sugar ensure you won’t end up with a dry, gritty muffin. 
  • Made with Wholesome Ingredients – I swapped some of the white flour with whole wheat, changed out canola oil for coconut oil, and swapped sour cream for greek yogurt. 
  • Customizable – I like to add various mix-ins like chocolate chips or even chunks of peanut butter cups! 
  • Easy way to use up ripe bananas! Sometimes I end up with way too many over-ripe bananas (never a problem in my opinion).This is a great alternative to a “regular” banana bread.  

Tips to Make the Best Healthy Banana Muffins:

  • Use ULTRA ripe bananas. I mean super brown and spotty. If your bananas are still mostly yellow, they are not ripe enough. 
  • I normally freeze my super ripe bananas. When I’m ready to use them, I take them out of the freezer and let them defrost in the refrigerator (make sure to put them in a bowl, otherwise you’ll end up with a mess in your refrigerator. 
  • Don’t skip the step of microwaving part of the mashed banana. This helps to break down the banana and create a more creamy texture. 
  • Beat the eggs and sugar until light and fluffy. The color should be a lighter yellow. In a stand mixer on medium-high speed this will take at least 5 minutes. With a hand mixer, you’ll probably have to do this for about 10 minutes. It might take longer depending on your mixer/speed. 
  • Don’t dump in the melted coconut oil at once. This is super important. You don’t want to deflate all of the air you whipped into the eggs! Drizzle it in slowly.

Modifications & Substitutions:

  • You can swap canola oil or vegetable oil for melted coconut oil
  • Feel free to use a combination of brown and white sugar – just make sure it doesn’t exceed the total units of sugar. 
  • If you want to use ONLY all purpose flour, feel free. You’ll end up with the same tender, moist loaf only without the whole wheat. 
  •  You can swap sour cream or creme fraisch for yogurt. However, I would not use fat free yogurt in this recipe.

How to Store Banana Muffins:

  • These muffins are best eaten the day-of! 
  • Keep them in an airtight container, and they’ll be good for up to 3 days. After a day or two, I would move them to the refrigerator. 
  • These muffins freezer great. Simply wrap each muffin in cling wrap and store in a gallon size freezer bag. They’ll last in the freezer for about three months. 
  • To Defrost/Reheat: Take them out to defrost at room temperature about an hour before you want to eat them. Alternatively, you can wrap them in tinfoil and bake at 400 degrees Fahrenheit for about 10 minutes until warm. 

If you like Healthy Chocolate Banana Muffins, you might also like: 

Healthy Low-sugar Banana Bread 


Healthy Chocolate Chip Banana Muffins

Made with whole wheat flour, greek yogurt, and reduced sugar. These healthy chocolate banana muffins are a perfect way to start the day!
Prep Time 30 minutes
Cook Time 25 minutes
Course Breakfast, Snack
Cuisine American
Servings 12
Calories 257 kcal


  • 1 12 cup muffin tin


Dry Ingredients

  • 1 cup (120 g) all-purpose flour
  • 1/3 cup + 2 teaspoons (55 g) whole wheat flour
  • 1/2 teaspoon baking soda
  • 1/2 teaspoon baking powder
  • 1/2 teaspoon Diamond Crystal kosher salt
  • 1 teaspoon cinnamon

Wet Ingredients

  • 3 large eggs
  • 6 tablespoons (75g) sugar
  • 1/3 cup coconut oil, melted and cooled to room temperature (substitute canola or vegetable oil)
  • 3 large super-ripe bananas (or 4 medium)
  • 6 tablespoons (90 g) whole milk Greek yogurt
  • 1 tablespoon vanilla extract

Optional Mix-Ins

  • 1 cup chocolate chips, sub chopped chocolate and/or chopped peanut butter cups
  • 1/3 cup walnuts, coarsely chopped and lightly toasted (optional)


  • Prep: Place a rack in the middle of the oven and preheat it to 350 degrees Fahrenheit. Butter and flour a standard 12-cup muffin tin, coat with nonstick cooking spray, or line with paper liners.
  • Toast Walnuts: Place the walnuts on a baking sheet and toast for 8 to 10 minutes until lightly toasted. Set aside to cool before chopping.
  • Whisk Dry Ingredients: In a medium bowl stir together the flour, baking soda, baking powder, salt, cinnamon, and set aside.
  • Beat Eggs & Sugar: Using a stand mixer fitted with a whisk attachment, beat the eggs and sugar on medium speed for approximately 5 minutes, or until light and fluffy. With an electric hand mixer this will take approximately 8 to 10 minutes.
  • Add the Oil: With the mixer on low speed, slowly drizzle in the coconut oil. Do not pour it in all at once, you want to add it slowly so it can incorporate with the eggs and not deflate the air you beat into them.
  • Break Down Bananas: In a medium microwave-safe bowl, mash all but one of the bananas completely with a fork and microwave for approximately 60 seconds or until hot.
  • Add Remaining Banana, Yogurt & Vanilla to Puree: With a small whisk, add the yogurt and vanilla to the banana puree and which to combine. Mash the remaining banana and stir it into the banana mixture.
  • Add Banana Mixture to Egg Mixture: Mix until just combined on a low speed.
  • Add Dry Ingredients to Wet: Fold the dry ingredients, nuts, and chocolate into wet ingredients by hand with a rubber spatula until thoroughly combined. There should be no streaks of flour.
  • Pour Batter into Prepared Pan: Using a small ice cream scoop or spoon, fill each muffin tin to the brim (be careful not to over-fill).
  • Bake the Muffins: Bake for 25 to 35 minutes until the muffins are golden brown on top and spring back lightly to the touch when you press them in the center. Allow the muffins to cool on a wire rack for approximately 10 minutes, and then remove them from the pan to cool entirely.
  • Storage: The muffins are best enjoyed the same day, but they can be stored at room temperature in an airtight container for up to 2 days. You can also store these in the freezer, tightly wrapped in plastic wrap for up to a month. To reheat from frozen, bake in an oven for 300 degrees Fahrenheit for 8 to 10 minutes.


Recipe adapted from Joanne Chang's Baking with Less Sugar Better than Flour Famous Banana Bread.
  • Whole greek yogurt - Substitute sour cream or creme fraiche (I do not recommend low fat or no fat). 
  • Whole wheat flour - If you don't want to use whole wheat (or not have it), simply use all-purpose flour for the entirety of the recipe. 
  • Walnuts - Substitute pecans or leave them out. You could also add another 1/3 cup of chocolate chips 🙂 
Keyword banana, recipe makeover

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