These Healthy Chocolate Chip Banana Muffins are made with wholesome ingredients like whole wheat flour, Greek yogurt, coconut oil, and reduced white sugar. You can feel good about starting your day with these tender, moist, and flavorful muffins—perfect for breakfast or a snack!
If you’ve found yourself with a surplus of ripe bananas and are looking for something healthier than your usual banana bread, these Healthy Chocolate Chip Banana Muffins are the perfect solution.Â
Unlike traditional banana muffins, which can be more like cupcakes, this recipe offers a light, tender muffin that’s naturally sweetened and made with wholesome ingredients.Â
The combination of whole wheat flour, Greek yogurt, and coconut oil creates a muffin that’s deliciously moist, while the addition of chocolate chips (or your choice of mix-ins) makes every bite irresistible.Â
Why You’ll Love These Healthy Banana Muffins
These muffins are the perfect balance of sweetness and nutrition. The tender crumb, moist texture, and wholesome ingredients make them a deliciously healthier choice.
- Tender & Moist: The muffins are light, soft, and never dry, thanks to the ripe bananas and Greek yogurt.
- Made with Wholesome Ingredients: By swapping out some of the white flour for whole wheat, using coconut oil instead of canola, and opting for Greek yogurt in place of sour cream, these muffins are a healthier option without compromising flavor.
- Customizable: Add your favorite mix-ins, like chocolate chips, toasted walnuts, or pecans.
- Great for Overripe Bananas: These muffins are a great way to use up those overripe bananas that have been sitting on your counter.

Tips for Making the Best Healthy Banana Muffins
- Use Very Ripe Bananas: For the best texture and flavor, use bananas that are super ripe with brown spots. If you freeze ripe bananas, let them thaw in the refrigerator before using.
- Microwave Part of the Mashed Bananas: This step helps break down the banana and creates a creamy texture for the batter.
- Beat Eggs and Sugar until Fluffy: The key to light muffins is to beat the eggs and sugar until they turn a light yellow. This will take about 5 minutes with a stand mixer (10 minutes with a hand mixer).
- Drizzle in the Coconut Oil: Add the melted coconut oil slowly while mixing to avoid deflating the air you’ve beaten into the eggs.
Modifications & Substitutions:
This recipe is straightforward and you can make some very easy swaps:
- Oil: You can substitute canola oil or vegetable oil for melted coconut oil.
- Sugar: A combination of brown and white sugar works fine, but make sure to stay within the total amount of sugar called for in the recipe.
- Flour: If you prefer, you can use all-purpose flour instead of whole wheat flour for a more traditional muffin.
- Yogurt Substitute: Sour cream or crème fraîche can be used in place of Greek yogurt, but avoid using fat-free versions for the best results.

How to Store Banana Muffins
These muffins are best enjoyed the day they’re made, but you can store leftovers in an airtight container for up to 3 days. If they last that long! After a couple of days, keep them in the refrigerator.
- Freezing: To store for longer, wrap each muffin in cling wrap and place them in a gallon-size freezer bag. They will last for about 3 months in the freezer.
- Reheating: Defrost at room temperature for an hour or wrap in foil and bake at 400°F for about 10 minutes until warm.
Got a lot of Bananas? You Should Try…
The Best Easy Banana Bread – Decadent and a classic comfort food!
Low Sugar Banana Bread – Another healthy alternative to “regular” banana bread
If you loved healthy chocolate banana muffins, don’t forget to leave a 5-star 🌟🌟🌟🌟🌟 rating in the recipe card below! We’d love to hear from you—leave a comment to let us know how you enjoyed it!

Healthy Chocolate Chip Banana Muffins
Equipment
- standard 12 cavity muffin tin
Ingredients
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, room temperature
- 6 tablespoons (75g) sugar
- 1/3 cup refined 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)
Instructions
- Prep pan and heat the oven: Place a rack in the middle of the oven and heat 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 the 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.
- Enjoy & Serve! 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. Freezing: 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.
Notes
- Whole greek yogurt - Substitute sour cream or creme fraiche (I do not recommend low fat or no fat).Â
- 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.Â
- Walnuts - Substitute pecans or leave them out. You could also add another 1/3 cup of chocolate chips 🙂Â