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The BEST Healthy Banana Muffins

BySamantha Skaggs February 17, 2025

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Healthy Banana Muffins are soft, sweet, and amazingly delicious, and they’re easy to make with wholesome ingredients including 100% whole wheat flour, Greek yogurt, and naturally sweetened with honey!

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If you enjoy tasty banana breads and muffins, you'll also love Banana Blender Muffins, Chocolate Banana Muffins, and Triple Chocolate Banana Bread!

There aren't many things quicker and easier for breakfast-on-the-go than good, old-fashioned muffins. They are also great as an after school snack or post-dinner treat. But let's face it...not all muffins are created equal, and not every muffin is inherently wholesome. In fact, some are actually more akin to cupcakes masquerading under the good name of 'muffin.' Lucky for us, these Healthy Banana Muffins are a step above the rest!

Ingredients

That's right, friends. These Healthy Banana Muffins are actually wholesome...and they're totally soft, moist, and tasty, to boot! And best of all, the ingredients are simple and straightforward:

Whole wheat pastry flour. When I want to add a wholesome boost to non-yeast baked goods such as pancakes, waffles, quick breads, and these Healthy Banana Muffins, I love to use whole wheat pastry flour. This 100% whole wheat flour is ground from soft white wheat for a softer, finer texture and lower protein than regular whole wheat flour (which typically comes from hard red wheat). As a result, whole wheat pastry flour yields baked goods with a texture that's closer to that of white flour. But despite tasting lighter, whole wheat pastry flour still retains the nutritional benefits of 100% whole wheat!
Baking powder + baking soda. For a perfect rise.
Salt. I prefer using fine sea salt.
Mashed banana. The riper, the better! It usually takes 5 average-sized bananas to yield 2 cups of mashed banana. You may need 6 bananas if they’re small, or only 4 if they’re particularly large.
Honey. I find that ½ cup honey is plenty in this recipe since ripe bananas are already very sweet, but you may increase the honey up to ¾ cup for sweeter muffins. Pure maple syrup may be substituted for the honey.
Oil. I prefer making this recipe with avocado oil, a neutral-flavored olive oil, or coconut oil (melted and cooled). However, you may substitute your favorite type of oil instead.
Eggs. At room temperature. Ingredients especially need to be at room temperature if you use coconut oil, as cold ingredients will cause the coconut oil to re-solidify. You can quickly warm up cold eggs by putting them in a bowl of warm water for a few minutes before cracking.
Pure vanilla extract. Because vanilla makes everything better!
Greek yogurt. Non-fat, low-fat, or full-fat Greek yogurt may be used. Or regular yogurt may be substituted for Greek yogurt.

For a tasty addition, 1 cup chopped nuts or mini chocolate chips may be stirred into the batter.

Healthy Banana Muffin recipe with liner removed.

How to Make Healthy Banana Muffins

(The below photos are intended to be helpful, but please refer to the recipe card at the bottom of this post for FULL DIRECTIONS.)

This Healthy Banana Muffin recipe is as easy to make as it is delicious!

Adjust rack to center position and preheat oven to 350°F. Prepare muffin pans by lining 24 muffin cups with paper liners.
In a medium bowl, whisk together the whole wheat pastry flour, baking powder, baking soda, and salt.

Whole wheat flour and other dry ingredients in bowl.

Dry ingredients combined for banana muffin recipe healthy.

. In a large bowl, combine the mashed banana with the honey, oil, eggs, and vanilla.

Mashed bananas, eggs, honey, and vanilla in bowl for heatlhy banana muffins recipe.

Add half of the flour mixture to the banana mixture and stir. Add the Greek yogurt and stir again.

Adding whole wheat flour mixture to wet ingredients for banana muffins healthy.

Add the remaining flour mixture and stir until just blended.

Adding remaining dry ingredients to healthy banana muffin recipe.

Banana muffin recipe healthy batter in bowl.

Divide the batter between the prepared muffin cups (using a cookie scoop can make this neater and easier), filling each muffin cup approximately ⅔ full with batter.

Scooping banana muffins healthy batter in muffin pan.

Healthy banana muffins recipe in pan ready for oven.

Bake for 14 to 17 minutes or until a toothpick inserted in the center of a muffin comes out clean.

Healthy Banana Muffins in pan fresh out of the oven.

Cool your Healthy Banana Muffins in the pans for a few minutes before turning them out onto wire rack to cool completely. Or enjoy warm with a pat of butter!

Why Make Healthy Banana Muffins?

When I have a bunch of browning bananas, sometimes I go in a decadent direction with them, from Baked Banana Donuts to Chocolate Chip Banana Bread.

Or sometimes I make a favorite breakfast recipe, such as Banana Breakfast Cookies or Banana Baked Oatmeal.

But more often than not, I bake up a big batch of these Healthy Banana Muffins. And the reasons are aplenty!

I know that they will give me a head start on breakfast over the next few busy mornings.
I know that they will be requested at snack time.
I know that they will taste delicious warm out of the oven or briefly reheated...with or without a pat of butter. 😉
And I know that I will feel good about feeding them to my family.

Storage

I typically keep these muffins in an airtight container on the counter for the first day or two. Then I transfer the container to the refrigerator, where they'll keep for about a week.

Alternatively, these Healthy Banana Muffins freeze beautifully! Place cooled muffins in a freezer-safe container or zip-top bag and freeze for up to 3 months. Thaw at room temperature or in the refrigerator. My daughter actually likes to pop a frozen muffin in a baggie in her backpack and it's thawed by snacktime!

Healthy Banana Muffins being removed from muffin liner.

Healthy Banana Muffins have been a family-favorite recipe ever since my kids were tiny. I hope you try them and love them, too!

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