This Whole Wheat Blueberry Muffin recipe delivers bakery-style muffins that are soft, tender, and filled with juicy, sweet blueberries.
This recipe for Whole Wheat Blueberry Muffins, just like my recipes for Carrot Cake Muffins and Pumpkin Muffins, is proof that whole wheat muffins don’t need to be dry or tasteless.
Kristen’s Key Takeaways
- Filled with the good stuff. Naturally sweetened, bursting with blueberries, dairy-free, and made with 100% whole grains. Perfect for a wholesome snack or breakfast–especially when paired with a homemade latte.
- Keep the blueberries suspended throughout the muffin. The secret to preventing the blueberries from sinking to the bottom of the muffins is to toss them with the flour mixture before folding in the wet ingredients.
- Use an ice cream scoop. It is the BEST tool for evenly scooping muffin batter into the muffin tin, without the mess!
Happy Cooking! xo Kristen
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.
- 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.
Allergy Modification
Egg Free Blueberry Muffins
To make these blueberry muffins egg-free (and vegan-friendly), mix together 2 tablespoons ground flaxseed with 1/3 cup water and let sit for 15 minutes. Use this mixture in place of the eggs in the muffin batter.
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 1/4 cup of the blueberry muffin batter.
- 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
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Heat oven to 350℉/175℃ and line a 12-cup muffin tin with muffin liners or grease well.
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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 1½ cups blueberries and toss to coat with flour.
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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.
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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.
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Scoop about ¼ cup of the batter into the prepared muffin tray.
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Bake for 22-25 minutes or until batter is set and toothpick comes out clean.
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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.
Flour Options: Whole white wheat, ivory wheat, and whole wheat flour all work perfectly for these blueberry muffins.
Egg Free and Vegan-Friendly Blueberry Muffins: Replace the eggs with flax eggs. For this recipe, you would need to mix together 2 tablespoons ground flaxseed with 1/3 cup water and let sit for 15 minutes.
Oil: Feel free to use canola oil in place of coconut oil. I prefer the taste of coconut oil to canola oil in baked muffins. It gives these muffins a bakery-quality taste and a slightly nutty flavor.
Frozen Blueberries: If using frozen blueberries, add them to the batter still frozen.
Calories: 211kcalCarbohydrates: 29gProtein: 4gFat: 10gSaturated Fat: 8gPolyunsaturated Fat: 1gMonounsaturated Fat: 1gTrans Fat: 0.003gCholesterol: 27mgSodium: 107mgPotassium: 210mgFiber: 3gSugar: 12gVitamin A: 57IUVitamin C: 2mgCalcium: 56mgIron: 1mg
Nutrition information is automatically calculated, so should only be used as an approximation.
This post was originally published in 2018 and updated in 2025.
