Whole Wheat Banana Muffins with Applesauce
I have a serious infatuation with muffins! They are one of my most favorite breakfasts. Moist, light and crumbly goodness crammed into a little fluffy muffin is pretty close to heaven for me, and these healthy banana muffins are NO exception.
They are made with whole wheat pastry flour, ripe bananas, applesauce and honey, with no butter, no eggs and no refined sugar. One bowl of dry, one bowl of wet and about 20 minutes in the oven is all it takes.

The Best Healthy Banana Muffins (Whole Wheat and Honey Sweetened)
I really can’t play favorites, though. I love my Pumpkin Muffins and Peach Muffins just as much. I think my muffin addiction must be hereditary, because my 2 year old daughter gets so excited while they’re baking! She keeps running over, looking in and pointing while saying “cookies.” Yes, my sweet girl, they are just as amazing as freshly baked cookies. My kids love these muffins, and recently I’ve been adding flax seed and chia seeds to make them power packed.
There is one ingredient that ABSOLUTELY makes these whole wheat banana muffins above and beyond perfect. No, not the bananas (they’re obviously important too). No, not the whole wheat pastry flour that I constantly rant and rave about (it’s vital also). It’s the pure vanilla extract! It’s only 2 teaspoons, but it makes these muffins out of this world. I love waiting close to the oven while they bake, because the pure, sweet vanilla aroma fills the air.
I do laugh when I see other recipes posing as “healthy” with lots of butter and sugar. These are sweetened with bananas and honey, and they still come out moist and fluffy.

Why You’ll Love These Banana Muffins
- Truly healthy. Whole wheat pastry flour, honey and applesauce, with no butter or white sugar.
- Light and fluffy. Whole wheat pastry flour keeps them tender, not dense.
- Big vanilla flavor. Pure vanilla extract makes them taste bakery fresh.
- Kid approved. Readers’ little ones love them as much as mine do.
What Readers Are Saying
“These are soooo good. We have made them a few times now and I can’t believe I am not eating the really sugary banana bread I love.”
Christina, a reader
“We made these muffins this morning and they were delicious!!”
Jeannette, a reader
“Instead of flax seed I used chia seeds. They are great! And my 1 year old loves them too, will make again.”
Alisa, a reader
Read all the comments or leave your own review below.
Ingredients You’ll Need
Here is what goes into these whole wheat banana muffins and why. Exact amounts are in the recipe card below.
- Whole wheat pastry flour: The key to light, fluffy whole grain muffins. Whole wheat pastry flour is milled from soft wheat, so it makes a tender crumb instead of a heavy one. A reader who always ground her own flour tried it and called the muffins amazingly fluffy.
- Baking powder and baking soda: Give the muffins their lift. The baking soda reacts with the acidic applesauce and honey for extra rise.
- Cinnamon and salt: Cinnamon warms up the banana flavor, and a little salt keeps the sweetness balanced.
- Flax seeds (optional): Add fiber and a nutty flavor. Chia seeds work too, and readers have swapped them in with great results.
- Bananas: Two bananas, peeled and mashed or blended. The riper they are, the sweeter and more flavorful your muffins will be, so use bananas with lots of brown spots.
- Applesauce: Replaces butter and adds moisture. Use unsweetened applesauce so the honey and bananas control the sweetness.
- Honey or organic agave: The only added sweetener. Honey also helps the muffins stay moist.
- Olive oil: A small amount keeps the crumb soft. Choose a light, mild olive oil.
- Milk: Any milk you like. I used vanilla almond milk. One reader had no milk and used yogurt watered down instead, and they still turned out great.
- Pure vanilla extract: The secret ingredient. Use pure vanilla, not imitation, for that sweet aroma and deep flavor. It also makes a great and classy gift for those difficult to shop for. Christmas, hostess gift, housewarming? Perfect gift idea.

How to Make Healthy Banana Muffins
- Heat the oven. Preheat to 375°F and lightly grease a muffin pan. Let the oven heat all the way so the muffins get a quick burst of rise when they go in.
- Mix the dry ingredients. In a large mixing bowl, combine the flour, baking powder, baking soda, cinnamon, salt and flax seeds. Whisk so the leaveners are spread evenly.
- Mix the wet ingredients. In a separate medium bowl, whisk together the bananas, applesauce, honey, olive oil, milk and vanilla until smooth. The mixture should be loose and fragrant.
- Combine. Add the wet ingredients to the dry ingredients and stir just to combine. A few small lumps are fine. Overmixing whole wheat batter makes muffins tough.
- Fill the pan. Scoop about 1/4 cup of batter into each muffin cup so they bake evenly.
- Bake. Bake for 20 to 23 minutes, or until the tops have browned. The inside will be moist! A toothpick in the center should come out with no wet batter.
- Cool. Let them cool in the pan for a few minutes, then move them to a rack so the bottoms don’t get soggy. They are delicious warm.
Kami’s tip: Don’t skip the pure vanilla extract. It’s only 2 teaspoons, but it is the one ingredient that takes these muffins from good to out of this world.

Top with a little natural peanut butter. Oh, it’s heaven.
Healthy Banana Muffin FAQs
- Can I use regular whole wheat flour? You can, but the muffins will be denser. Whole wheat pastry flour is what keeps them light and fluffy.
- Can I use chia seeds instead of flax seeds? Yes. Readers have used chia seeds with great results, and I’ve been adding both lately.
- Can I make them gluten free? A reader whose husband eats gluten free made a gluten free version and loved them. Use a gluten free all purpose flour blend in place of the whole wheat pastry flour.
- What if I don’t have milk? A reader used yogurt watered down instead and said they were great.
- How do I know when they are done? Bake 20 to 23 minutes, until the tops have browned. The inside stays moist.
- Can I use agave instead of honey? Yes. The card calls for honey or organic agave, so use whichever you have on hand.
- How do I store banana muffins? Keep them in an airtight container in the refrigerator and enjoy within 3 to 4 days, or freeze them for longer storage.
- Can I freeze them? Yes. Cool completely, freeze in a freezer bag and thaw overnight in the fridge or warm briefly in the microwave.

Need more healthy breakfast ideas? Try my Breakfast Quiches. You can make a dozen or two and freeze them for up to 3 months, or refrigerate them for 3 to 4 days. They are my husband’s favorite! And if you love a classic, try the Homemade Blueberry Muffins from Scratch on our sister site, Everything Muffins.

Healthy Banana Breakfast Muffins
Ingredients
- 2 cups whole wheat pastry flour
- 2 teaspoons baking powder
- 1/2 teaspoon baking soda
- 1 teaspoon cinnamon
- 1/4 tsp salt
- 2 tsp flax seeds optional
- 2 bananas peeled and mashed (or blended)
- 1/2 cup applesauce
- 1/2 cup honey or organic agave
- 1/4 cup olive oil
- 1/4 cup milk of your choice... I used vanilla almond milk
- 2 tsp pure vanilla extract
Instructions
- Preheat the oven to 375 degrees.
- In a large mixing bowl combine all the dry ingredients.
- In a separate medium-sized bowl, whisk together the bananas, applesauce, honey, olive oil, milk, and vanilla.
- Add the wet ingredients to the dry ingredients and stir to combine.
- Fill lightly greased muffin pan with about 1/4 cup mixture. Bake for 20 to 23 minutes or until the tops have browned. The inside will be moist!
Made these muffins? Leave a star rating in the recipe card and tell me how they turned out in the comments below. I love hearing about your swaps, whether it is chia seeds, yogurt or a gluten free flour blend!

mmm I love banana muffins! These look so so good!
Ohmyheck KAMI!!! I have MISSED commenting on your blog – goodness gracious girl things have been wild! I am so sorry – but I still have been checking you out and you’ve had some AWESOME recipes coming my way. These look so yummy I’m definitely trying them – along with quite a few other things you’ve recently posted. Thanks for sharing your recipes! Thanks for making them TRUELY healthy 🙂 None of that “healthy… this and that.. with 1 1/2 c. white sugar…” jazz – you are the real deal girlie!
Thanks, Yvonne! I do laugh when I see other recipes posing as ‘healthy’ with lots of butter and sugar. Thanks for your sweet comment.
We made these muffins this morning and they were delicious!! I have tried your cranberry orange and blueberry banana muffins in the last week or so, and these were my favorite so far. I just tried the WW pastry flour, I’ve always ground my own, and can add my stamp of approval there….amazingly fluffy. 😉 Can’t wait to try more. Thanks!
Thanks for your kind comment, Jeannette! I definitely love light and fluffy muffins and WW pastry flour has become essential when making them.
My husband eats gluten free so I made a gluten free version today, and we LOVED them! I put a link to your site and this recipe on my blog, here’s the link if you want to check it out. Thanks for the great recipes!
https://thereislifeafterwheat.blogspot.com/2014/02/healthy-and-delicious-banana-muffins.html
Thank you for the feedback, Celeste! I will definitely check it out.
These are soooo good. We have made them a few times now and I can’t believe I am not eating the really sugary banana bread I love. It is so good to eat something and not have to feel so guilty
Yay, Christina! I love hearing this type of feedback.
Just made these, I didn’t have milk so used some yogurt and watered it down. Instead of flax seed I used chia seeds. They are great! And my 1 year old loves them too, will make again.
YAY! Thank you for sharing your success! My kids (4 years old and 16 months) loves these muffins too. Recently, I’ve been adding flax seed and chia seeds to make them power packed. Thanks again for your comment!