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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!

5 Star Review

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

— Charlotte —

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 (like this Vegan Pumpkin Bread). 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 (like my famous One Bowl Brownies), no mixer required.
Banana Chocolate Chip Muffins. Easy, vegan, and healthy!

How to Make Healthy Banana Chocolate Chip Muffins

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 (as are these Buttermilk Blueberry Muffins). I’ve even taken them with me to the gym a few times if I’m running errands right afterward and need a healthy snack to tide me over until my next full meal.

The Ingredients

  • Banana. Have a few overripe bananas sitting on your counter? They’re the perfect addition to these healthy banana chocolate chip muffins that adds sweetness, potassium, and fiber.
  • Flaxseed Meal. My swap for eggs makes these banana chocolate chip muffins vegan in addition to being healthy and wholesome. (This Vegan Zucchini Bread is another vegan favorite.)

Substitution Tip

If you do not need these muffins to be vegan you can swap the flax “egg” for one large egg.

  • Applesauce. One of my best muffin hacks (as seen in these Applesauce Muffins) for cutting back the oil content without sacrificing moisture.
  • Canola Oil. While the applesauce can reduce fat in muffins, I like to keep a little oil in the recipe. Its fat content helps keep the muffins soft and tender.
  • Coconut Sugar. My new obsession in baking (especially for Banana Bars). If you’ve never baked with coconut sugar before, it’s a great natural sugar made from coconut palm sap that’s a great alternative to traditional cane sugar.

Substitution Tip

Regular light brown sugar may be used in place of the coconut sugar if that’s what you have on hand and are accustomed to baking with.

  • Maple Syrup. Another natural sweetener that adds a subtle maple flavor to these muffins and pairs perfectly with the ripe bananas and chocolate chips.
  • Vanilla. Enhances and elevates.
  • White Whole Wheat Flour. My favorite stealthy healthy sneak for all sorts of muffins and baked goods (like these Vegan Pumpkin Muffins) to add extra protein, fiber, and iron to the recipe.
  • Baking Soda. For some lift and fluff.
  • Cinnamon. For a little warm, earthy spice and aroma.
  • Chocolate Chips. Dark chocolate chips are my fav for healthy banana muffins like these (and Chocolate Zucchini Muffins). They put a little chocolatey goodness into every bite without overdoing the sugar.
Healthy Banana Chocolate Chip Muffins. Easy, moist, and kid friendly!

The Directions

  1. Mix the flaxseed meal with water and let stand for 5 minutes. (If you are using a regular egg, you can skip this step).
  2. Mash the bananas.
  3. Add the applesauce, oil, and flax “egg” (or regular egg if not using flax) to the bananas.
  4. Whisk in the coconut sugar, maple syrup, and vanilla.
  5. Add the baking soda, cinnamon, salt, and flour. Stir until barely combined.
  6. Fold in the chocolate chips.
  7. Divide the batter into a standard-size muffin tin.
  8. Bake until a toothpick inserted in the center of a muffin comes out clean and the tops spring back lightly when touched.
  9. Let cool in the pan briefly before removing the muffins and letting cool completely on a wire rack. ENJOY!

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.

Recommended Tools to Make Healthy Banana Chocolate Chip Muffins

No matter how many different muffin 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!

Frequently Asked Questions

Can I Make Healthy Banana Chocolate Chip Muffins Gluten Free?

I haven’t yet experimented with making these muffins gluten free. If you’d like to try it, I would recommend starting with a 1:1 baking blend like this one.

How Do You Adapt This Banana Muffin Recipe for High Altitude?

I’m sorry. I’m not familiar with the conversion process for high-altitude baking so I can’t, unfortunately, provide specific advice for making healthy banana chocolate chip muffins at a high altitude.

Are Chocolate Chips Vegan?

Not always. If you follow a vegan diet, I recommend always checking your labels to confirm the chocolate chips you are purchasing are 100 percent vegan.

Healthy Banana Chocolate Chip Muffins

4.98 from 35 votes
Moist healthy banana chocolate chip muffins with applesauce. Easy, vegan, and whole wheat, this easy muffin recipe is perfect for on the go!

Prep: 10 minutes
Cook: 25 minutes
Total: 35 minutes

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.



  • *INGREDIENT NOTE: 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.
  • GLUTEN FREE: I haven’t yet experimented with making these muffins gluten free. If you’d like to try it, I would recommend starting with a 1:1 baking blend like this one.
  • TO STORE: 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.
  • TO FREEZE: Muffin can be kept frozen for up to 3 months in a freezer-safe container or resealable freezer bag.


Serving: 1muffinCalories: 176kcalCarbohydrates: 31gProtein: 3gFat: 5gSaturated Fat: 2gPolyunsaturated Fat: 1gMonounsaturated Fat: 2gTrans Fat: 1gCholesterol: 1mgPotassium: 190mgFiber: 3gSugar: 14gVitamin A: 21IUVitamin C: 3mgCalcium: 44mgIron: 1mg

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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 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. I made these gluten free and they were delicious! I shared with my coworkers and they all loved them! I’ll definitely make them again. A new favorite.5 stars

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