Healthy Blueberry Muffins are fluffy, moist, and pack as many blueberries as possible! Make ahead or eat fresh out of the oven for a nutritious breakfast or snack.

We also love these healthy lemon blueberry muffins and healthy blueberry banana 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 for healthy breakfast or snack.

Moist, light and so fluffy, both kids and adults love these healthy muffins and you will love them too!

Why You’ll Love This Recipe

  • 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, this recipe uses maple syrup or honey which means less sugar than your giant coffee shop muffins.
  • Low oil: Unsweetened applesauce not only keeps them moist, it lowers the use of heavy oils for lighter, better for you blueberry muffin!
  • Delicious: Usually, I prefer to eat my berries fresh, however these muffins deserve even the priciest supermarket January blueberries!

Ingredients for Healthy Blueberry Muffins

Blueberries, applesauce, baking powder, baking soda, whole wheat flour, eggs, cinnamon, salt, oil, maple syrup, vanilla, cooking spray.
  • Flour: You can use whole wheat flour or spelt flour.
  • Blueberries: I made these muffins 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 muffins will be sweeter. Here is a great Instant Pot applesauce recipe.
  • Eggs: Provide lift and binding.
  • Any oil: Healthy widely available options are avocado oil, melted coconut oil, grapeseed oil or extra virgin olive oil.
  • 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: Use pure vanilla extract and not artificial for the best flavor.
  • Cinnamon: Adds a warm taste and light spice to the muffins.
  • Baking staples: Baking powder and baking soda for texture, and salt to bring out flavors of all other ingredients.

How to Make Healthy Blueberry Muffins

Easy to make in one bowl, here is a quick overview how to make this healthy blueberry muffin recipe.

Step by step process how to make healthy blueberry muffins.
  • Combine wet ingredients and leavening agents: In a large bowl, add eggs, applesauce, maple syrup, oil, vanilla, cinnamon, baking powder, baking soda, and salt and whisk well. Ensure the baking powder and soda have completely dissolved.
  • Add dry ingredients: Add flour and stir gently just until mixed, don’t overdo it. You can also let batter sit for 3 minutes to absorb the moisture, then give 1-2 final stirs.
  • Add berries: Add blueberries and stir a few times just enough to incorporate them into the muffin batter.
  • Bake: Using large ice cream scoop, fill muffin tin with muffin batter. Bake for 22 minutes or until toothpick inserted in the middle comes out clean. Cool in the muffin pan for 30 minutes before transferring onto a cooling rack to cool more.
Muffins in red tin cooling on top of stove.

Tips for Best Results

  • Mix batter only until combined: 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.
  • 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 the muffins. They keep cooking with residual heat in a muffin tin.
  • Let them cool completely: These 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 blueberry muffins and bake for 11-13 minutes. Do a toothpick test.

How to Store and Freeze

To store: Muffins won’t last more than 2 days because they are so good! Store them in an airtight container placed in a cool dry place for 3-4 days.

To freeze: 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.


What flour can I use?

In this recipe, you cannot use any other flour except for whole wheat flour or spelt flour. Whole wheat pastry flour or white whole wheat flour may work. If you try, please let me know. Using all-purpose flour or gluten free flour will need adjustment of the recipe. Baking is a science and it’s best to follow the recipe.

Can I make these muffins without eggs?

Yes, to make these muffins egg-free and also vegan, you can use an equivalent amount of flax eggs or chia seed eggs and be sure to use maple syrup.

Can I use yogurt instead of applesauce?

Yes, while you can use an equal amount of plain regular yogurt or Greek yogurt instead of applesauce, be prepared for less sweet muffins. You can try to add a few more tablespoons of sweetener with hopes this won’t offset the batter consistency. I recommend to use applesauce though.

Can I use frozen blueberries?

Yes, no need to thaw the frozen blueberries. 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 Blueberry Recipes You’ll Love

More Healthy Muffin Recipes

Healthy blueberry muffins in a red silicone muffin tin with fresh berries around them.
Four healthy blueberry muffins.

Healthy Blueberry Muffins

These Healthy Blueberry Muffins are fluffy, moist, and pack as many blueberries as possible! Made in one bowl for healthy breakfast or snack.
4.97 from 142 votes
Servings 12 muffins
Calories 221
Diet Vegetarian
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 parchment paper muffin liners or use silicone muffin pan (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 tablespoon flour, add to the batter and give a few stirs.
  • Using large ice cream scoop, fill 12 openings of a muffin pan 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 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.
  • Freeze: Bake and cool muffins completely. Arrange in a single layer in a resealable plastic bag or any container with a lid. Freeze for up to 3 months.
  • Do not overmix batter: Stir a few times, let batter sit and stir again. A few dry flour patches are fine.


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
    Great recipe! Classic blueberry muffin but not overly sweet. Just made a few changes based on preference. Swapped one flax egg, used half apple sauce and half yogurt, and used half ap flour. This gave me 17 regular sized muffins. I baked them in metal tins with silicone liners, in which case 17 minutes was good for bake time.

  2. Hi! These taste delicious! I added nuts to them, and tried an apple pecan, and banana walnut version too. They took much longer to cook through, and were kinda mushy inside and dried out on the outside. Any idea what I did wrong and how to fix it?

4.97 from 142 votes (21 ratings without comment)

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