by Olena

Healthy Blueberry Muffins

Olena's image
Olena Osipov
5 from 123 votes

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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 these and freeze some for later. Other favorites include these almond flour blueberry muffins and healthy blueberry bread.

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 husbands love these and healthy strawberry muffins! They are perfect right out of the oven and leftovers are perfect 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!

I recommend to buy organic whenever you can because berries are on a Dirty Dozen list. And if you can’t find fresh, frozen work too, just like in blueberry oatmeal crumble bars!

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.
  • 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 muffin recipe to always have a wholesome healthy breakfast idea 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.

Quinoa breakfast bake, a side of breakfast potatoes, and egg muffins would all be great for a light lunch or brunch spread in addition to these muffins.

How to Store and Freeze

To store: These 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.

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.
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!
4.96 from 123 votes
Print Save Rate
Course: Muffins
Cuisine: North American
Diet: Low Fat
Prep Time: 5 minutes
Cook Time: 20 minutes
Cooling Time: 30 minutes
Total Time: 55 minutes
Servings: 12 muffins
Calories: 221kcal
Author: Olena Osipov



  • 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.
  • Yogurt: You can use equal amount of plain regular or Greek yogurt.
  • 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

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222 comments on “Healthy Blueberry Muffins

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  1. 5 stars
    I just had to tell you how good these muffins are! I used frozen mixed berries because that’s all I had on hand and they taste great. The consistency of the muffins is so fluffy, yet filling. I don’t think anyone would even guess they’re healthy!

  2. 5 stars
    Can a different berry be used besides blueberries? My daughter doesn’t like blueberries sadly. Looks delicious and how long will the muffins be good for after baking? 3 days or so?

  3. 5 stars
    Olena, I feel the same as you do about feeling bad for baking fresh berries -but with figs! They are so hard to get where I live that when I do find some, all I want to do is enjoy them raw! Alas, perhaps I will never make fig baked goods. 🙂

  4. 5 stars
    This sounds terrific! However, it seems that the directions are missing a lot of steps. Will you please clarify?

    1. Hi Ashley.I just double checked and nothing is missing. You must have gotten confused at “add eggs through salt”. Just add all ingredients starting from eggs and ending with salt. Follow the recipe further.:)

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