These healthy blueberry muffins use honey and whole wheat flour to replace highly processed sugar and white flour, adding irresistible nutty and floral flavors. A 100% whole wheat blueberry muffin that tastes amazing? Yes, please!

a half of a blueberry muffing stacked on top of two a whole blueberry muffin on a plate.
Photo Credits: Mark Beahm

These healthy blueberry muffins are an incredible breakfast or mid-afternoon treat. Like our Healthy Breakfast Egg Muffins and Spanakopita Egg Bites, they’re sized for one and self-contained, making them convenient and portable.

When you look at the nutrition of most blueberry muffins, they’re essentially cupcakes without frosting, which means they are decidedly not Mediterranean Diet friendly. However, these healthy whole wheat blueberry muffins break the mold by using more flavorful and wholesome ingredients. They’re nutty, fluffy and bursting with fresh blueberry flavor without all the added sugar.

I like to bake and freeze these muffins on the weekend or a night when I find some extra time. I pack one for work and, by lunchtime or my coffee break, it’s thawed and ready to go! Not only do I get a delicious homemade muffin, but I also have a snack that fuels the rest of my afternoon rather than nosedives me into a sugar slump.

Table of Contents
  1. What Makes a Healthy Muffin?
  2. Ingredients for Healthy Blueberry Muffins 
  3. What is White Whole Wheat Flour?
  4. How to Make Healthy Blueberry Muffins
  5. How to Store Whole Wheat Blueberry Muffins
  6. What to Serve with Blueberry Muffins
  7. More Quick and Healthy Breakfast Ideas
  8. Buttery, Smooth Italian Extra Virgin Olive Oil–Perfect for Baking!
  9. Healthy Blueberry Muffins Recipe

What Makes a Healthy Muffin?

When developing this recipe I decided to stay away from refined sugar and refined flour. Instead I used honey and 100% whole-grain flour for a boost in fiber, protein, and micronutrients. According to the USDA, "100 grams of whole wheat flour [about ⅔ cup] contains 10 to 12 grams of fiber, while an equal amount of refined (white) flour contains 2 to 3 grams of fiber."

So if you're not sold on using 100% whole wheat flour start with a 50/50 ratio of whole wheat and white flour. You'll still increase the fiber content and stay full longer. Then you can progressively increase the amount of whole wheat flour and reduce the white flour over time.

Blueberries are well known for their exceptional antioxidant content and extra virgin olive oil is considered one of the healthiest oils available. Butter is usually called upon to create a tender muffin, but applesauce is a great substitute, and I use it here.

So for this recipe, I used unsweetened applesauce to give these muffins extra moisture without the addition of butter. The natural sweetness from the applesauce also helps reduce the need for lots of sugar.

ingredients for healthy blueberry muffins including white whole wheat flour, baking powder, baking soda, salt, cinnamon, honey, apple sauce, olive oil, milk, an egg, vanilla extract and blueberries.

Ingredients for Healthy Blueberry Muffins 

These blueberry muffins may have a slightly longer ingredient list than your standard blueberry muffins recipe. It’s worth it: they’re full of nutritious pantry ingredients you can easily find at the store if you don’t have them already. Here is what you’ll need to get started:

  • White whole wheat flour: A healthy and flavorful whole grain flour that becomes fluffier than standard whole wheat flour. King Arthur is fairly easy to source, but you can substitute with 1 cup whole wheat flour mixed with ¾ cup all-purpose flour if necessary. Whole Wheat Pastry flour is also a great option.
  • Baking powder and baking soda: Leavening agents that give the muffins their soft and airy texture. 
  • Kosher salt: Even in sweeter recipes, salt is a flavor enhancer that brings out the best of the other ingredients.
  • Cinnamon: Just a hint of cinnamon adds some nuance to the nutty whole wheat and sweet blueberries.
  • Honey: A natural, unrefined sugar. It is also a humectant, meaning it helps to keep the muffins moist for days. Use a high quality honey, like our Alfa Honey from Crete with tasting notes of fresh thyme. 
  • Apple sauce: Unsweetened apple sauce adds moisture to the batter.
  • Extra-virgin olive oil: Less processed than other vegetable oils, extra-virgin olive oil is rich in antioxidants and micronutrients. It also has a beautiful fruity and floral flavor. I like to use a smooth, buttery olive oil, like our Nocellara
  • Milk: You can use any whole, skim, low fat, or plant-based milk you prefer. You could also substitute with Greek yogurt, but the muffins will be denser.
  • Egg: A whole egg is used as a binder, giving structure and holding the ingredients together. Feel free to use a flax egg instead, but the muffins won’t be quite as fluffy.
  • Blueberries: Fresh blueberries work best, but you can use frozen in a pinch. You will need to adjust the baking time a few minutes longer. If using frozen, the muffin batter may take on a blueish hue.
  • Vanilla extract: The flavor of the whole wheat flour and blueberries is enhanced by a small amount of vanilla extract.

What is White Whole Wheat Flour?

It may sound like white whole wheat flour is a flour blend, bleached whole wheat flour, or partially sifted. In reality, it genuinely is an unbleached whole grain.

To make white whole wheat flour, millers use a hard white wheat berries. It’s nutritionally equivalent to red whole wheat flour but lighter in color and less bitter. By using white whole wheat flour, you benefit from the boost in nutty flavor and nutrition (fiber, vitamins, and minerals) without any of the dryness or bitterness.

a several blueberry muffins stacked on a plate.

How to Make Healthy Blueberry Muffins

Making healthy blueberry muffins couldn’t be easier. The batter comes together in less than 10 minutes and the muffins are ready to eat within the hour. Be sure to let the batter rest after mixing to hydrate the flour and improve the texture. You can do this while the oven finishes preheating.

  • Get ready: Preheat the oven to 375°F. Lightly grease a standard 12-cup muffin pan or line with cupcake liners.
  • Mix the dry ingredients: In a large mixing bowl, whisk together 1 ¾ cups white whole wheat flour, 1 teaspoon baking powder, ½ teaspoon baking soda, ½ teaspoon salt, and ¼ teaspoon cinnamon.dry ingredients for blueberry muffins mixed together in a bowl with a whisk.
  • Mix the wet ingredients: In a separate bowl, whisk together ½ cup honey, ½ cup apple sauce, ⅓ cup olive oil, and ¼ cup milk. Add 1 large egg and 1 teaspoon vanilla extract and whisk until fully combined.wet ingredients for blueberry muffins mixed together in a bowl with a whisk.
  • Combine: Pour the wet ingredients into the dry ingredients. Use a rubber spatula to fold the batter together until just combined. Do not overmix. It’s okay if there are a few lumps.
  • Fold in the blueberries: Stir in 1 ½ cups blueberries with the spatula. Let the batter stand for 20 minutes to allow the flour to hydrate. blueberries added to blueberry muffin batter in a bowl with a rubber spatula.
  • Divide the batter: Scoop or pour the batter into the prepared muffin pan. Divide the batter evenly among the wells, until each is about ¾ full.healthy blueberry muffin batter in a muffin tin.
  • Bake: Bake for 22 minutes, or until a toothpick inserted into the center of one of the muffins come out clean.baked healthy blueberry muffins in a muffin tin.
  • Cool: Let the muffins cool in the pan for 10 minutes, then turn them out onto a wire rack to cool completely. If any muffins are stuck, run a butter knife around the edge of each muffin to free them from the pan. 6 blueberry muffins on a cooling rack.
  • Serve: Enjoy immediately. Or, transfer to an airtight container at room temperature or freezer bag in your freezer to store. a blueberry muffin split in half on a plate.

How to Store Whole Wheat Blueberry Muffins

The muffins will keep in an airtight container at room temperature for up to 4 days. To freeze the muffins, place them in a freezer-safe container or freezer bag. They will keep for up to 3 months. Uncover and thaw frozen muffins on the counter.

What to Serve with Blueberry Muffins

These healthy muffins are welcome at any brunch or special occasion breakfast. Though they feel celebratory, they’re also an excellent make-ahead breakfast for busy mornings.

Serve them on their own for a small snack. Or, they’re especially indulgent with jam and a drizzle of honey, compote, or fresh fruit and a hot cup of coffee or tea, like our Arabic Tea With Fresh Mint.

More Quick and Healthy Breakfast Ideas

Browse all Mediterranean recipes.

Visit Our Shop.

A bottle of extra virgin olive oil.

Buttery, Smooth Italian Extra Virgin Olive Oil–Perfect for Baking!

Extra Virgin Olive Oil from hand-picked, cold-extracted Nocellara olives.

5 from 16 votes

Healthy Blueberry Muffins

photo of author mark beahm.Mark Beahm
a several blueberry muffins stacked on a plate.
These healthy blueberry muffins swap out refined sugar and flour for wholesome ingredients that are rich in both nutrients and flavor. Make ahead for a quick breakfast or snack on the go.
Prep – 10 minutes
Cook – 22 minutes
Resting Time 30 minutes
Total – 1 hour 2 minutes
Cuisine:
American
Serves – 12 muffins
Course:
Breakfast, Dessert, Snack

Ingredients
  

  • 1 ¾ cups (210g) white whole wheat flour
  • 1 teaspoon baking powder
  • ½ teaspoon baking soda
  • ½ teaspoon kosher salt
  • ¼ teaspoon ground cinnamon
  • ½ cup honey
  • ½ cup unsweetened apple sauce
  • cup olive oil, plus more for coating the tray
  • ¼ cup milk
  • 1 large egg
  • 1 teaspoon vanilla extract
  • 1 ½ cups fresh or frozen blueberries

Instructions
 

  • Get ready: Preheat the oven to 375°F. Lightly grease a standard 12-cup muffin pan or use muffin tin liners.
  • Whisk the dry ingredients: In a large bowl, whisk together the flour, baking powder, baking soda, salt, and cinnamon.
  • Whisk the wet ingredients: In a medium bowl, whisk together the honey, apple sauce, olive oil, milk, egg, and vanilla extract until fully combined.
  • Fold together: Pour the wet ingredients into the dry ingredients and fold with a spatula until just combined. Do not overmix. It’s okay if there are a few lumps.
  • Add the blueberries: Stir in the blueberries with the spatula to distribute through the batter.
  • Divide the batter: Scoop or pour the batter into the prepared muffin pan, dividing them evenly among the wells. Fill each well to about ¾ full.
  • Bake the muffins: Bake for 22 minutes, or until a toothpick inserted into the center of one of the muffins come out clean.
  • Cool the muffins: Let the muffins cool in the pan for 10 minutes, then turn them out onto a wire rack to cool completely. Run a butter knife around the edge of each muffin to free them from the pan if necessary.
  • Serve: Serve warm or at room temperature. The muffins will keep in an airtight container at room temperature for up to 4 days.

Video

Notes

hoelIf you don’t have white whole wheat flour, you can substitute with wcup whole wheat flour mixed with ¾ cup all-purpose flour. 
  • Mixing muffin batter activates the gluten and causes it to develop and become more elastic. Mix until the ingredients are just combined. Overactive gluten doesn’t rise and can lead to tough, dense, and dry muffins.
  • The muffins will keep in an airtight container at room temperature for up to 4 days. They can also be frozen in a freezer-safe container or freezer bag for up to 3 months. Thaw frozen muffins on the counter.
  • Visit our shop to browse quality Mediterranean ingredients including olive oilshoneyjams and spices.

Nutrition

Calories: 178.6kcalCarbohydrates: 28.2gProtein: 3.2gFat: 6.9gSaturated Fat: 1gPolyunsaturated Fat: 0.7gMonounsaturated Fat: 4.6gTrans Fat: 0.002gCholesterol: 14.3mgSodium: 186.1mgPotassium: 61.9mgFiber: 2.4gSugar: 14.7gVitamin A: 41.1IUVitamin C: 2mgCalcium: 42.5mgIron: 0.7mg
Tried this recipe?

Share it with the world

Mark learned to bake professionally at Two Fat Cats Bakery in Portland, Maine and was most recently the head baker at Hjem Kensington, a Danish café in London. He lived in Barcelona and Madrid for six years, before moving to London and then back to the States. He is fascinated by the intersection of food, culture, and science. He has been developing recipes for home bakers for three years and began writing for The Mediterranean Dish in 2022.

When he’s not in the kitchen, he spends his time traveling, knitting, and learning to throw pottery.
Learn More

Get our best recipes and all Things Mediterranean delivered to your inbox.

Leave a comment

Your email address will not be published. Required fields are marked *

How many stars would you give this recipe?




This site uses Akismet to reduce spam. Learn how your comment data is processed.

Comments

  1. 5 stars
    A note to others who might be lazy like me and not read the whole recipe! (Lol)! There is a typo in the written instructions above. In the written instructions in the paragraphs above the actual recipe is says "Add 3/4 cups of flour" instead of "1 3/4 cups". I was lazy and didn't read the whole recipe, so I made this with only 3/4 cups of flour. It did cross my mind that the batter was super thin, but I figured I would "trust the process", ha! Obviously these muffins didn't turn out. My own fault, but I wanted to let others know. READ THE WHOLE RECIPE! It should be 1 3/4 cups of flour. Don't be me.

    1. Hi, Jennifer! I'm Summer and I work here at The Mediterranean Dish. Thank you for pointing that out. We've corrected it in the recipe. I do hope you you try these muffins again. They are so delicious!

  2. I'm needing more grab-and-go breakfast options for my son but he has Celiac. May need to try with gluten free flour or a 1/2 gluten free flour and 1/2 almond flour mixture. I'll report back if I try. 🙂 I make Suzy's banana bread recipe from her cookbook with the gluten free flour substitution and it always comes out perfect!

    Thank you for sharing!