Healthy Banana and Chocolate Chip Muffins with yogurt are easy to make, have less sugar, and are perfectly moist. You can use traditional yogurt or a dairy free alternative. These muffins are great for kids and enjoyed by the whole family.

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Why You’ll Love These
- Quick, easy, and a delicious afternoon snack or to-go breakfast.
- Super moist, with plenty of baking tips for extra high muffin tops.
- Chocolate chips make it feel like an extra special treat.
- Full of nutritious ingredients and whole grains.
Recipe Ingredients
For these healthy chocolate chip banana muffins, you’ll need mostly pantry staples and a few other basic ingredients. Here’s a look in more detail of what we need:
- whole wheat pastry flour – you can use whole wheat pastry flour, whole wheat white flour, or a mix of whole wheat and all-purpose flour. Whole wheat pastry flour will yield the softest muffins. This recipe wasn’t tested with grain-free flours. If you’re looking for a grain-free / gluten free muffin, try Almond Flour Banana Muffins!
- baking soda – baking soda gives these muffins a nice muffin top dome.
- sea salt – salt enhances that banana flavor.
- fresh bananas – overripe bananas add natural sweetness and moisture! Use extra spotty, even black, for the most flavor.
- pure maple syrup – maple syrup adds the right amount of sweetness we all love in a muffin recipe. If your bananas are a little on the underripe side or you have a sweet tooth, you can add 1/4 cup granulated sugar, like white sugar, brown sugar, or coconut sugar.
- yogurt – use plain Greek yogurt, Skyr yogurt, or traditional. If you are dairy free, an almond milk, cashew milk, or coconut milk yogurt will also work. Sour cream is a good sub if that is all you have on hand.
- large eggs – regular eggs give these muffins structure and lift. I have not tested this chocolate chip banana muffin recipe with a flax egg, but you can try these Healthy Banana Muffins instead.
- vanilla – pure vanilla extract makes the best banana chocolate chip muffins.
- milk of choice – go for dairy-free milk, like unsweetened almond milk or coconut milk, or regular dairy milk. Measure it out in a measuring cup while you prepare the rest of the ingredients
- chocolate chips – I like a mix of mini chocolate chips and regular dark chocolate chips, but use whatever you have on hand.
Find the full detailed instructions with measurements in the recipe card below, at the end of this post.

How to Make Chocolate Chip Banana Muffins
These chocolate chip banana muffins are so easy, I bet you’ll start making these on a weekly basis. Here’s a step-by-step overview of how they are made!
Mix Dry Ingredients
Preheat the oven to 425ºF and spray a 12-cup muffin tin with cooking spray. In a medium bowl, whisk together the whole wheat flour, baking soda, and salt.
NOTE: If using parchment paper muffin liners, you may want to lightly spray with coconut oil spray to prevent too much sticking, since this recipe does not have any oil in it. I also like silicone muffin cups, which don’t need spraying.
Whisk Wet Ingredients
In a large bowl combine mashed bananas with maple syrup and granulated sugar, if using. Then, whisk in yogurt, eggs, and vanilla until smooth.

Make Banana Muffin Batter
Slowly add half of the flour mixture to the banana mixture, gently stir a few times, then add milk, and then remaining flour. Fold in chocolate chips.
TIP: Careful not to over-mix or you’ll end up with tough muffins.

Fill Muffin Pan
Evenly distribute batter into prepared pan with an ice cream scoop, filling each muffin cup about 2/3 way full. Top with extra chocolate chips if you want some to show in the muffin tops.
Bake
Bake muffins in the preheated oven set to 425ºF for 5 minutes, then drop the oven temperature down to 350ºF and continue baking for 10-15 minutes, or until golden brown. Cool slightly on a wire rack before enjoying.

Serving Suggestions
These banana chocolate chip healthy muffins are delicious just as is, maybe cut in half and slathered with some butter, for an easy breakfast. We like to enjoy them both warm and cold from the fridge. Some of my favorite ways to serve include:
- Jam / Jelly
- Nut Butter, like peanut butter or almond butter
- Glass of milk
- Hot cup of coffee

How to Store & Reheat
Leftover muffins will keep in an airtight container at room temperature for the first day, then stored in the fridge for 2-3 days.
Freeze: Place the muffins in a zip top freezer bag, squeeze out as much air as possible, and freeze for up to 3 months. Thaw at room temperature or overnight in the fridge.
Reheat: Pop a muffin in the microwave for 10-15 seconds, or warm in the toaster oven for just a few minutes.

Recipe Tips & Notes:
Check Greek yogurt banana muffins at 10 minutes with a toothpick inserted into center of muffins. Muffins are done when no wet batter is present on the toothpick, or just a few crumbs. If you have a little bit of wet batter on the toothpick, bake another 2 minutes then check again, to prevent from overbaking.
Baking the muffins first at 425ºF will lend itself to a higher rise for the tops of the muffins, AKA MUFFIN TOP! But you can bake straight at 350ºF for 20 minutes, if preferred.
If you want to make mini muffins, bake at 350ºF and start checking for doneness at the 10-minute mark.
If you want to transform these muffins into banana bread, prepare the recipe as written, then use a loaf pan and bake at 375ºF for about 25 minutes, then check every 10 minutes for wet batter. You may need to cover the top with foil to prevent too much browning.

Recipe FAQs
How do I know if my bananas are ripe enough?
You will know the bananas are ripe when they have a bunch of brown spots all over, or are almost black, and are super soft. Overripe bananas provide a natural sweetness so that we can use less sugar (or no sugar at all).
How do I freeze these banana muffins?
Cool the muffins completely, then transfer a plastic freezer bag and squeeze out as much air as possible. Label, date, and freeze for up to 3 months. Thaw in the fridge or at room temperature.
How can I make gluten-free banana chocolate chip muffins?
I have not tested this recipe with a 1:1 gluten-free baking flour blend, but I suppose it will work. Bob’s Red Mill is a great brand.
What makes these banana muffins healthy?
These muffins are made with whole grain flour, protein-packed Greek yogurt, real maple syrup (although you can omit), and minimal to no added sugar thanks to sweet ripened bananas. It is a simple list of healthy ingredients you can feel good about.
More Banana Recipes You’ll Love:
If you make this Healthy Banana Chocolate Chip Muffins recipe, be sure to leave a comment and star rating on the blog! I love hearing from you, and it helps others learn more about the recipe too. Xx Ashley
Yogurt Banana Chocolate Chip Muffins
Ingredients
- 1 ¾ cups whole wheat pastry flour, see notes
- 1 teaspoon baking soda
- ¼ teaspoon salt
- 1 cup well-mashed extra ripe bananas, (about 2 medium bananas)
- ¼ cup pure maple syrup
- ¼ cup granulated sugar, can omit
- ⅔ cup plain Greek yogurt or Skyr yogurt
- 2 large eggs
- ½ tablespoon vanilla extract
- ¼ cup milk of choice
- ⅔ cup chocolate chips, plus more for topping (I used mix of mini and regular sized)
Instructions
- Preheat oven to 425ºF and line muffin pan with paper liners, or spray with oil; set aside.
- Mix Dry Ingredients: In a medium bowl whisk together dry ingredients; set aside.
- Mix Wet Ingredients: In large bowl combine well-mashed banana with maple syrup and granulated sugar, if using. Whisk in yogurt, then add eggs and vanilla, whisking until smooth. Slowly add in half of the flour, gently stir a few times then add milk, remaining flour and fold in chocolate chips. Careful not to over-mix or you’ll end up with tough muffins.
- Bake: Evenly distribute batter into prepared pan, filling about 2/3 way full. Top with more chocolate chips if you want some to show in the muffin tops. Bake muffins at 425ºF for 5 minutes. Then drop oven temp down to 350ºF and continue baking for 10-15 minutes. Check muffins at 10 minutes with inserted toothpick. Muffins are done when no wet batter is present on the toothpick.
- Allow muffins to cool in pan for a few minutes before transferring to rack to cool completely.











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