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You won't believe these Blueberry Muffins are actually good for you! Made with whole grains, naturally sweetened, and bursting with plump blueberries, these Whole Wheat Blueberry muffins are tender, moist, and perfectly sweet.
Good For You Blueberry Muffins
These Whole Wheat Blueberry Muffins (just like my Carrot Cake Muffins and Pumpkin Muffins) prove that whole wheat baked goods don't have to be dry, bland, or packed with sugar to taste amazing.
Made with 100% whole wheat flour, a touch of oil, and naturally sweetened with maple syrup, these muffins are tender, bakery-soft, and just the right amount of sweet. Applesauce helps keep the muffins light and moist, while the blueberries add bursts of juicy flavor that pair perfectly with the maple.
They're wholesome, satisfying, and downright delicious!
Happy Cooking! xo Kristen
Recipe Highlights
Notes on Ingredients
You will find the full list of ingredients, along with quantities in the recipe card. Below are a few tips to help you make the right selection.
- Blueberries: Use fresh or frozen blueberries. When working with with frozen berries, do not defrost before adding to the batter.
- Coconut Oil: Melted coconut oil adds a rich, nutty undertone to the muffin. Feel free to to use canola oil in place of coconut oil.
- Applesauce: The applesauce cuts down on the amount of oil that is needed to be added to the batter, while ensuring the blueberry muffin turns out soft and tender.
- Maple Syrup: Pure maple syrup is the perfect natural sweetener, as the flavor compliments the blueberries' natural flavor. However, you can swap it out for honey.
- Whole Wheat Flour: While this recipe is designed to be made with whole wheat flour, it works well with whole white wheat flour, all-purpose flour, or 1:1 gluten-free flour.
How to Make Whole Wheat Blueberry Muffins
This recipe for blueberry muffins comes together easily, and you will find detailed instructions in my recipe card. However, I do want to walk you through a few expert tips to ensure your blueberry muffins turn out fluffy, moist, and delicious.
- Combine dry ingredients. Whisk or sift together flour with baking powder, baking soda, and salt together.
- Add blueberries to flour mixture. And then toss them to coat--this is key to keeping the blueberries suspended throughout the muffins.
- Combine wet ingredients. Whisk together the applesauce, eggs, oil, and vanilla together.
- Don't overmix batter. Add the wet ingredients to the dry ingredients and fold the ingredients together using a wooden spoon or spatula until JUST combined and the flour is fully moistened. You don't want to overmix, as this will activate the gluten and result in dense, tough muffins.
- Portion muffins. Fill each muffin cup with about ¼ cup of the blueberry muffin batter.
Kristen's tip
Use an ice cream scoop to portion out the muffin batter. It is the BEST tool for evenly scooping muffin batter into the muffin tin, without the mess!
- Bake Until Set. You want to bake the muffins until the tops of the muffins are puffed up and just set.
Storing Whole Wheat Muffins
It is important to note that because these blueberry muffins are made with whole grains and no preservatives, so it is best to refrigerate or freeze them, rather than storing the muffins at room temperature.
- Refrigerate: Let the muffins cool fully and then transfer then to an airtight container and refrigerate for up to 5 days.
- Freeze: Place the cooled muffins on a cookie sheet and freeze for 30-60 minutes until solid. Once frozen solid, transfer the muffins to a freezer-safe bag or container and store them in the freezer for up to 3 months. Defrost in the fridge overnight, or warm in the microwave for 1-2 minutes to heat before serving.
More Delicious Muffin Recipes
- Peanut Butter Banana Muffins
- Pumpkin Banana Muffins
- Cranberry Orange Muffins
- Chocolate Zucchini Muffins
- Chocolate Chip Oatmeal Muffins
Did you make this recipe?
If you enjoyed this recipe, please leave a comment with a 5-star review at the bottom of the post. Thank you!
Whole Wheat Blueberry Muffins
Video
Ingredients
- 2 cups whole wheat flour
- ¼ teaspoon table salt
- 2 teaspoons baking powder
- ½ teaspoon baking soda
- 1 ½ cups blueberries, washed and dried
- 2 large eggs, see note for egg-free recipe
- 1 teaspoon pure vanilla extract
- ½ cup melted and cooled coconut oil, or canola oil
- ½ cup pure maple syrup, or honey
- 1 cup unsweetened applesauce
Instructions
- Heat oven to 400℉ (200℃) and line a 12-cup muffin tin with muffin liners or grease well.
- In a large bowl whisk 2 cups whole wheat flour, ¼ teaspoon table salt, 2 teaspoons baking powder, and ½ teaspoon baking soda together. Add 1 ½ cups blueberries and toss to coat with flour.
- In a separate small bowl, whisk together 2 large eggs, 1 teaspoon pure vanilla extract, ½ cup melted and cooled coconut oil, ½ cup pure maple syrup, and 1 cup unsweetened applesauce together until combined.
- Make a well in the center of the flour mixture and pour in the wet ingredients. Fold the wet and dry ingredients together until the flour is fully moistened, but do not overmix.
- Scoop about ¼ cup of the batter into the prepared muffin tray.
- Bake for 14-17 minutes or until batter is set and toothpick comes out clean.
- Cool the muffins on a cooling rack for 10-20 minutes and then remove the muffins from the muffin tin. Serve or cool completely before storing.
Equipment
Notes
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
This post was originally published in 2018 and updated in 2025.
These are great! Hearty whole wheat and natural sweeteners plus blueberries from our garden, what is not to love? We will make these again!
Lucky you with blueberries in your garden! I love it! Thanks for taking the time to share the review, Carole 🙂
Wow, these are so delicious!! The perfect texture and level of sweetness. I used mashed banana instead of applesauce since that's what I had on hand and used half vanilla extract and half almond extract. Turned out amazing, will be making these again!
Thank you for sharing your review and modifications! I love hearing you enjoyed these muffins!
I love finding healthy baked good recipes! This is a tasty recipe and easy to make too. I was short on applesauce, so I used non-fat Greek yogurt to make up the rest. It worked just fine.
Thanks for sharing your modification, Lisa! And taking the time to leave a review. I appreciate it!
Shoot, I don’t have applesauce. Can I use more of any of the other ingredients to sub it out?
Hi Abby! You could use mashed banana (keep in mind it will add a banana flavor to the muffins), or you could use plain yogurt.
Can I use egg whites instead of eggs?
Yes! You would need to use 3 egg whites to replace the 2 whole eggs. Enjoy!
These muffins were so delicious. They were a great grab and go breakfast, or something yummy to snack on for the day. They did not last long in my house!
These muffins are delicious, however I’ve totaled the calories up and each muffin is actually over 200 kcal. That’s a LOT of difference. Just FYI.
Hi Joyce! I am so glad you enjoyed the blueberry muffins. The nutrition card states each muffin is just over 200 calories. I am not sure what your calculation showed or where the discrepancy was.
I have regular all-purpose flour, could I use that instead? Would any adjustments be needed?
Hi Shenna! That will work just fine in this recipe. No changes needed.