Healthy Double Chocolate Banana Muffins

This incredible muffin recipe comes from the AK archives back in 2017 and reading back on the post was such a fun trip down memory lane. I wrote it right after Tony and I got engaged, and am reposting it now that we are married in a new home with THREE little boys!

Time truly flies, but perfect healthy chocolate banana muffins are still the ultimate treat.

These muffins are a take on my famous Skinny Banana Chocolate Chip Muffins but with a chocolate twist that seriously makes them taste like chocolate cake. I originally made them after receiving the sweetest note from a woman named Sara and her (then) 4-year-old daughter, Reagan. Sara described Reagan as a true little chef and baker who was truly amazing in the kitchen. They had a glorious baking day after finding my banana chocolate chip muffins and emailed me the kindest note and cutest photo.

I whipped up the best-ever chocolate version of those muffins just for Reagan, who is now 10! Whether or not they see this post update, it’s so fun to think back on that memory and the ways that Ambitious Kitchen has touched so many lives over the years.

SO, get a baking day on your calendar, make a batch of these chocolate beauties, and have yourself a wonderful week.

healthy double chocolate banana muffins in a muffin tin

What makes these chocolate banana muffins healthier?

Traditional chocolate banana muffins, while absolutely delicious, are typically made with lots of refined sugar and butter or oil. I lightened these babies up a bit by sweetening them with just 1/4 cup of honey and ripe, mashed bananas so that they’re refined sugar free. You’ll also only need 2 tablespoons of oil because the muffins get extra moisture from protein-packed greek yogurt! They also have a boost of whole grains thanks to whole wheat pastry flour instead of white flour.

Ingredients in the best healthy chocolate banana muffins

While they are chocolate muffins, they’re made with whole grains, protein packed greek yogurt, naturally sweetened with honey (or maple syrup) and contain just a hint of chocolate sweetness. I call them perfection. Here’s what you’ll need to make them:

  • Bananas: be sure to use super ripe bananas with lots of brown spots to get the perfect amount of sweetness and banana flavor.
  • Honey: we’re also adding a little honey to boost the sweetness. You can also use pure maple syrup if you’d like.
  • Egg: you’ll need one egg in this muffin recipe.
  • Oil: a couple tablespoons of olive oil to add moisture.
  • Yogurt: a little yogurt adds additional moisture and a boost of protein. Feel free to use plain or vanilla 2% yogurt or whole milk greek yogurt.
  • Flour: you’ll need whole wheat pastry flour to give the muffins that fluff factor.
  • Cocoa powder: for the ultimate rich chocolate flavor. Be sure to use high quality cocoa powder or cacao powder for the best flavor!
  • Baking staples: don’t forget the vanilla extract, baking soda, and salt.
  • Chocolate chips: gotta have that melty chocolate in every bite. Don’t forget to sprinkle the muffins with a few chocolate chips on top, too.

I love to top them with a dollop of peanut butter because everyone knows PB + chocolate = life.

healthy chocolate banana muffins on a wire rack

Optional ingredient swaps

As with all baking recipes, I suggest sticking with the recipe as best as possible to ensure that they come out perfectly every time. Here are a few ingredient swaps I can recommend:

  • For the oil: feel free to use avocado oil, melted & cooled coconut oil, or melted butter or vegan butter in place of the olive oil.
  • For the yogurt: 2% plain greek yogurt adds the best moisture, but nonfat yogurt or dairy-free yogurt should also work well.
  • For the flour: feel free to use white whole wheat flour or a mix of whole wheat flour and all purpose flour.

Can I make them gluten free?

I’ve only tested these muffins using whole wheat pastry flour or a mix of whole wheat flour and all purpose flour, so I cannot recommend a gluten-free substitute. Feel free to try my Paleo Double Chocolate Tahini Banana Muffins instead!

What about vegan?

I haven’t tested a vegan version of these muffins either, but you could try swapping the egg for 1 flax egg, and using your favorite plain or vanilla dairy free yogurt. Then be sure to use maple syrup instead of the honey as well as dairy free chocolate chips. Let me know in the comments if you try it!

the best healthy chocolate banana muffins on a wire rack

Try a healthy chocolate banana bread

I think these healthy chocolate banana muffins can be made into a bread, too! Simply pour the batter into an 8×4 inch loaf pan greased and lined with parchment paper. Bake for 40-55 minutes until a toothpick comes out clean.

Alternatively, try one of these delicious chocolate banana bread recipes:

Storing & freezing tips

  1. To store: store these chocolate banana muffins on the counter in an airtight container for a day, then transfer them to the fridge for up to 4-5 days. The muffins get even fudgier after sitting in an airtight container for a day; they sweeten up a bit and get super soft.
  2. To freeze: place the muffins in an airtight container or reusable bag and freeze for up to 3 months. When you’re ready to eat them, you can microwave them for 45 seconds-1 minute or until warm.

healthy chocolate banana muffin with a bite taken out

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If you make these healthy chocolate banana muffins, be sure to leave a comment below and rate the recipe! You can also snap and picture and post it on Instagram using the hashtag #ambitiouskitchen. And of course be sure to follow Ambitious Kitchen on Instagram. xo!

Healthy Double Chocolate Banana Muffins

4.94 from 65 votes

healthy chocolate banana muffin with a bite taken out

Prep Time 10 minutes

Cook Time 25 minutes

Total Time 35 minutes

Healthy double chocolate banana muffins made with whole grains and naturally sweetened with honey and ripe bananas. These healthy chocolate banana muffins are perfectly moist and made in one bowl for an easy breakfast or snack! Freezer-friendly and absolutely delicious.


  • 3 medium ripe bananas, mashed
  • 1/4 cup honey or pure maple syrup
  • 1 teaspoon vanilla extract
  • 1 large egg
  • 2 tablespoons extra virgin olive oil (can sub melted and cooled coconut oil, avocado oil or butter)
  • 1/2 cup plain or vanilla 2% or whole-milk greek yogurt
  • 1 cup whole wheat pastry flour or white whole wheat flour*
  • 1/2 cup unsweetened cocoa powder or cacao powder (use a high quality cocoa powder)
  • 1 teaspoon baking soda
  • ¼ teaspoon salt
  • 1/2 cup chocolate chips, plus 2 tablespoons for sprinkling on top


  1. Preheat oven to 350 degrees F. Line a 12 cup muffin tin with muffin liners and spray with nonstick cooking spray.

  2. In a large bowl add the mashed bananas, honey, vanilla, egg, oil and greek yogurt. Whisk wet ingredients together until well combined.

  3. Add dry ingredients to wet ingredients: whole wheat pastry flour, cocoa powder, baking soda and salt. Mix until combined. Stir in 1/2 cup of chocolate chips.

  4. Pour batter into greased muffin cups. Sprinkle the remaining 2 tablespoons of chocolate chips on top of muffins. Bake for 23-27 minutes until the tester comes out clean.

Recipe Notes

*You can use a mix of regular whole wheat flour and all purpose, but these are best when made with whole wheat pastry flour or white whole wheat flour.


Servings: 12 muffins

Serving size: 1 muffin

Calories: 180kcal

Fat: 8.1g

Saturated fat: 3.6g

Carbohydrates: 27.8g

Fiber: 4.1g

Sugar: 13.4g

Protein: 4.6g

Recipe by Monique Volz | Photography by: Sarah Fennel

This post was originally published on January 3rd, 2017, and republished on April 20th, 2023.