Healthy Blueberry Muffins made with whole wheat flour, maple syrup and applesauce are fluffy, moist, and absolutely delicious! Make ahead or eat fresh out of the oven for a nutritious breakfast or snack.

Healthy muffin recipes are easy to make, so double and freeze some for later. Other favorites include these lemon blueberry muffins and almond flour blueberry muffins.

Four healthy blueberry muffins on a counter with fresh blueberries.

These healthy blueberry muffins come out fantastic every time. With no refined sugar and nutrient dense ingredients, I can feel good about feeding these to my family.

Moist, light and so fluffy, both kids and adults love these blueberry muffins and healthy blueberry bread! Perfect right out of the oven and leftovers are great for healthy snacks.

Usually, I prefer to eat my berries fresh, like on this healthy french toast casserole or served with Ukrainian sweet lazy pierogi. However, these blueberry muffins deserve even the priciest supermarket January blueberries!

What Makes These Blueberry Muffins Healthy?

  • Whole grain flour: By using 100% whole wheat or spelt flour these muffins are full of nutrients plus fiber.
  • Naturally sweetened: Skip the refined white sugar, these muffins use maple syrup or honey which means less sugar overall than your giant coffee shop muffins.
  • Low oil: Unsweetened applesauce not only keeps these muffins moist, it lowers the use of heavy oils for lighter, better for you blueberry muffin!

Ingredients You Will Need

Blueberries, applesauce, baking powder and soda, whole wheat flour, eggs, cinnamon, salt, oil, maple syrup, vanilla, cooking spray.

My healthy blueberry muffins recipe contains simple ingredients:

  • Whole wheat or spelt flour: Baking is a science and it’s best to use whole wheat or spelt flour only for this recipe. Using all purpose or gluten free flour will need adjusting the recipe and I haven’t tried. Whole wheat pastry flour or white whole wheat may work, if you try, please let me know.
  • Blueberries: My favorite homemade blueberry muffins are with fresh blueberries but frozen blueberries can be used with great success just like in blueberry oatmeal crumble bars.
  • Applesauce: I use unsweetened applesauce but if sweetened is all you can find, that works. Your muffin will just be sweeter. Here is a great Instant Pot applesauce recipe as well.
  • Eggs: Provide lift and binding, see recipe notes for egg free.
  • Any oil: Healthy widely available options extra virgin olive oil, avocado oil, coconut oil (melted first).
  • Liquid sweetener: Maple syrup or honey. Please do not use any dry sweetener. It will throw off batter consistency and recipe will not work.
  • Vanilla extract: Pure, not imitation for best taste.
  • Cinnamon: Adds a warm taste and light spice to the muffins.
  • Baking staples: Baking powder, baking soda, and salt.

How to Make Healthy Blueberry Muffins

Easy to make in one bowl, you may want to double this healthy blueberry muffins recipe to always have a wholesome healthy breakfast on hand for your own family!

Liquid muffin ingredients with a whisk in a blue bowl.

Combine liquids and leavening agents first by whisking them well in a large mixing bowl. Ensure your baking powder and soda have completely dissolved.

A spatula in a blue bowl stirring flour into liquid ingredients.

Then add flour and stir gently to mix. Do not over mix your batter as additional gluten will develop and result in dense muffins.

A few patches of flour are OK and better than perfectly smooth batter. You can also let it sit for 3 minutes or so to absorb moisture. Then give 1-2 final stirs.

Blueberries and muffin batter in blue bowl with spatula.

Add blueberries and give a few stirs just enough to incorporate into the muffin batter.

Fill muffin tin using large ice cream scoop with your muffin batter. Bake for 22 minutes or until toothpick inserted in the middle comes out clean.

Cool in the tin for 30 minutes before transferring onto a cooling rack to cool more or enjoying.

Tips for Best Results

  • Mix batter only until combined. Stir a few times and let batter sit for a few seconds to let flour absorb the moisture. Stir again. A few flour patches here and there are fine.
  • Keep an eye on muffins while they bake. All ovens vary and I recommend to check your muffins 3 minutes to the end. If toothpick comes out clean, time to remove muffins. They keep cooking with residual heat in a tin.
  • Let muffins cool completely. These blueberry muffins are delicate, light, and fluffy. If you don’t let them cool patiently for 30 minutes, they will deform and fall apart a bit.
  • Mini muffins: You can make mini muffins and bake for 11-13 minutes. Do toothpick test. You might also love to make these healthy blueberry pancakes!
Muffins in red tin cooling on top of stove.

Can I Use Frozen Blueberries?

Yes. Frozen berries are a great way to make healthy blueberry muffins during cooler months. No need to thaw the frozen blueberries.

However, if you are worried about them turning your batter blue, rinse them a few times under cold water, then gently pat dry. Fold them gently into your muffin batter and give a few stirs. Once you notice some blueberry streaks stop stirring to prevent further bleeding.

More FAQs

Can I use gluten-free flour?

In this recipe, you cannot substitute any other flour except for whole wheat flour and spelt flour. Try these almond flour blueberry muffins or healthy blueberry breakfast cake for gluten-free options.

Can I make these egg-free?

Yes, to make these muffins egg free and also vegan, you can use an equivalent amount of flax egg or chia seed egg.

Can I substitute the applesauce?

Yes. You can use an equal amount of plain regular yogurt or Greek yogurt like I do in healthy blueberry banana muffins or healthy lemon blueberry muffins.

How do I prevent blueberries from “sinking”?

I did not find blueberries sinking to the bottom of muffins. If you do, next time toss them with 1 tbsp of flour in a separate bowl before adding to batter.

What Can I Serve These Muffins With?

Make healthy fruit salad while waiting for your muffins to cool off. It goes great with fresh baked muffins!

Or spread some peanut butter or cream cheese on top.

How to Store and Freeze

To store: Healthy blueberry muffins won’t last more than 2 days because they are so good! Store muffins in an airtight container placed in a cool dry place for 3-4 days or in the fridge up to a week.

Freeze muffins: Bake and cool muffins completely. Then arrange them in a single layer in resealable plastic bag or any container with a lid. Freeze for up to 3 months.

To reheat: Thaw on a counter for a few hours. Warm up in the oven at 350 F or microwave for 30 seconds for that freshly baked experience.

Storage Tip

Don’t miss my detailed posts how to store muffins and how to freeze muffins to make sure your leftover muffins stay fresh longer.

Enjoy these healthy blueberry muffins! Would love to know if your kids approved!

More Healthy Muffin Recipes

And if you love a good healthy pie, check out this gluten free blueberry pie.

Blueberry muffins in a red muffin tin.
Four healthy blueberry muffins.

Healthy Blueberry Muffins

Healthy Blueberry Muffins made with whole wheat flour, maple syrup and applesauce are fluffy and moist plus easy to make in one bowl!
4.97 from 141 votes
Servings 12 muffins
Calories 221
Diet Low Fat
Prep Time 5 minutes
Cook Time 20 minutes
Cooling Time 30 minutes
Total Time 55 minutes



  • Preheat oven to 425 degrees F and line muffin tin with unbleached muffin liners or use silicone muffin tin (I used both and didn't spray anything).
  • In a large mixing bowl, add eggs, applesauce, maple syrup, oil, vanilla, cinnamon, baking powder, baking soda, and salt. Whisk well to combine, making sure baking powder and soda have dissolved. Add flour and stir gently to mix. Do not over mix.
  • In a small bowl, toss blueberries with 1 tbsp flour, add to the batter and give a few stirs.
  • Using large ice cream scoop, fill 12 openings with batter. Bake for 10 minutes, reduce oven temperature to 375 degrees F, and bake for another 10 minutes or until toothpick inserted in the middle comes out clean.
  • Remove from the oven and let muffins cool in the tin for at least 30 minutes before transferring onto a cooling rack to cool more or enjoy.



  • Store: Store in an airtight container in a cool dry place for up to 3 – 4 days or in a fridge for up to a week.
  • Freeze: Bake and cool muffins completely. Arrange in a single layer in resealable plastic bag or any container with a lid. Freeze for up to 3 months.
  • A: You can use equal amount of plain regular or Greek yogurt to replace applesauce.
  • Gluten-free? Unfortunately only flours that will work in this recipe are the ones listed.
  • Do not overmix batter: Stir a few times, let batter sit and stir again. A few dry flour patches are fine.
  • Egg free: Learn how to make a flax egg or chia seed egg.


Serving: 1muffin | Calories: 221kcal | Carbohydrates: 34g | Protein: 4g | Fat: 8g | Saturated Fat: 1g | Trans Fat: 0.003g | Cholesterol: 27mg | Sodium: 177mg | Fiber: 4g | Sugar: 15g
Course: Muffins
Cuisine: North American
Author: Olena Osipov
Did you make this recipe?Mention @ifoodreal or tag #ifoodreal!

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About Olena

Welcome! I grew up in Ukraine watching my grandma cook with simple ingredients. I have spent the last 11 years making it my mission to help you cook quick and easy meals for your family!

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  1. 5 stars
    Excellent…I rarely have a recipe hit the target first time. I followed exactly…they were perfect…light delicious..not too sweet..not heavy. Best recipe! I’ll be trying other recipes you have now. Thank you for sharing.

    1. Awe, you are so welcome, Diana! So happy to hear you are enjoying my recipes! Please don’t be shy to leave me a comment with a star review once you make any recipe. Have a great week!

  2. 5 stars
    This is a fantastic recipe, thank you for sharing! My little boy was super into blueberries…and then not so much after I bought a bunch of organic blueberries at the store on sale. So I needed to use them, but I’m super picky about feeding him healthy treats. This was perfect! If you ever make a version with lemon incorporated (juice and maybe zest), I’d love to see that. These muffins turned out beautifully with 1 1/3 C sprouted organic Spelt flour and 1 C Whole Wheat flour, and I went with the maple syrup option. B/c of my abundance of blueberries, I did use 2 C (knowing that it’s on me if it’s too much), but they turned out perfect! Thank you again for sharing this recipe.

  3. Hi, I noticed that you mentioned yogurt in your notes, but I didn’t see any yogurt listed in the ingredients or the directions. Just curious if it was accidentally left out?
    Thanks, Debra

  4. 5 stars
    Such an awesome recipe. Along with the blueberries I added Frozen cherries, unsweetened coconut and walnuts. Yum

  5. 5 stars
    These are my family’s favourite blueberry muffins of all time and have been for quite awhile! So fluffy & perfect.
    I did notice that you changed the recipe and increased the amount of sweetener, oil, and flour, and I’m just curious as to why? And won’t it now make more than 12 muffins?

    1. The amounts for the ingredients are correct as listed and will make 12. But feel free to use 1/3 c maple syrup, 1/4 cup oil, 2 cups flour if you wish.

  6. 5 stars
    These are fantastic! For people asking about gluten free, I’ve made 4 dozen now using King Arthur’s Measure for Measure and following the recipe exactly otherwise. I’d recommend weighing the flour (280g). They have turned out so well gluten free. I can only imagine how wonderful the gluten versions must be. Thank you!

  7. 5 stars
    I haven’t tried this yet, but just wanted to say thank you! For one, so much information and such details makes your recipes fool proof. And, such varieties! For another, you do indicate if substitutions can be made and offer alternatives. I had bookmarked a TON of recipes and recipe sites because I need gluten and sugar free. Now, I will only go to your website, plus I have your recipes delivered to my inbox as well. No more searching for recipes that I can make and eat! And no more compromising on taste. Thank you dear Olena!

  8. Hi, if i make these blueberry muffins mini how long do i cook them for? and at the same temperature?

    1. Yes I would do 5 at the higher temp, then 3 min at lower temp, check, then 2 min more etc until toothpick test indicates done.

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