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Made with whole grains, naturally sweetened, and bursting with plump blueberries, these Whole Wheat Blueberry Muffins are tender, moist, and perfectly sweet.
Love blueberries? Don't miss my recipes for Lemon Blueberry Coffee Cake, Blueberry Pie Bars, and Blueberry Smoothie.
Whole Wheat Blueberry Muffins at a Glance
- Yield: 12 muffins
- Time Needed: 15-minute prep + 15-minute bake
- Healthier Ingredients: Whole wheat flour, maple syrup, and fresh or frozen blueberries
- Allergy-Friendly: Works with 1:1 gluten-free flour; naturally dairy-free, and can be made egg-free and vegan-friendly
- Why This Recipe Works: Using both applesauce and maple syrup keeps the muffins moist and tender while allowing them to be made with 100% whole wheat flour and less added fat.
Recipe Highlights
Kristen's Keys to Healthy Blueberry Muffins
I've been making healthier baked goods for my family for decades, and these are the tricks I rely on to keep whole wheat muffins moist, fluffy, and kid-approved.
- Applesauce is key. It works to keep the batter moist, adds natural sweetness, and cuts back on the amount of oil needed.
- Measure the flour with care. The most accurate way to measure flour is to use a digital kitchen scale. But if you don't have a scale, spoon the flour into your measuring cup, then level it off. Scooping the flour directly from the canister or bag can lead to using too much, resulting in dense muffins.
- Toss the blueberries with flour. Tossing the berries with the dry ingredients rather than folding them into the batter helps prevent them from sinking to the bottom of the muffins.
- I recommend using coconut oil. Coconut oil keeps these muffins incredibly moist and adds subtle richness.
For more soft, fluffy, bakery-style muffins using whole wheat flour and without refined sugars, don't miss my family's favorite whole wheat pumpkin muffin recipe and whole wheat carrot cake muffins.
Happy Cooking! xo Kristen
Notes on Ingredients & Substitutions
- Blueberries: Use fresh or frozen blueberries. When working with frozen berries, do not defrost before adding to the batter.
- Coconut Oil: If you enjoy the flavor of coconut, use unrefined coconut oil for a slight nutty sweetness. Otherwise, refined coconut oil keeps the muffins moist and is essentially flavorless. If you don't have coconut oil, you can use canola oil, vegetable oil, or even melted and cooled unsalted butter.
- Applesauce: Use unsweetened store-bought, homemade applesauce, or Instant Pot applesauce.
- Maple Syrup: Pure maple syrup is the perfect natural sweetener, as the flavor complements 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, I have tested the recipe with whole white wheat flour, all-purpose flour, and a 1:1 gluten-free flour blend, and all work well.
- Egg: Helps to bind the muffins together. To make these muffins egg-free, combine 2 tablespoons ground flaxseed with 6 tablespoons water and let sit for 5 minutes, then use the flax egg in place of the eggs in the batter.
How to Make Whole Wheat Blueberry Muffins
- Combine dry ingredients. Whisk together the flour, baking powder, baking soda, and salt in a large mixing bowl.
- Add the blueberries to the flour mixture and toss to coat. This helps keep the berries suspended throughout the muffins.
- Combine wet ingredients. Whisk together applesauce, eggs, oil, and vanilla.
- Fold wet and dry ingredients together. Add the wet ingredients to the dry ingredients and fold them together with a wooden spoon or spatula until JUST combined and the flour is fully moistened.
- 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 are puffed up and just set. A sure-fire way to know muffins are fully cooked is to insert a digital thermometer into the center of the muffin. They are done when they reach 200°F to 205°F.
Storage Instructions
Because these blueberry muffins are made with whole grains and no preservatives, it is best to refrigerate or freeze them rather than store them at room temperature.
- Refrigerate: Let the muffins cool fully and then transfer them 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
Packed with whole grains and bursting with fresh blueberries, these Whole Wheat Blueberry muffins are tender, moist, and perfectly sweet.
Video
Ingredients
- 2 cups whole wheat flour, See note on measuring
- ¼ teaspoon table salt
- 2 teaspoons baking powder
- ½ teaspoon baking soda
- 1½ 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
- 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 1½ 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 or the internal temperature of the muffins reaches 200°F (100℃).
- 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
Measuring Flour: Spoon and level flour into your measuring cup. For the most accurate results, weigh the flour. You will need 120 grams of flour for every cup of flour. As this recipe is written, that would be 240 grams of flour.
Flour Options: In place of whole wheat flour, you can use whole white wheat, ivory wheat, all-purpose flour, or even a 1:1 gluten-free flour blend. Measure as directed above.
Egg Free: For every egg, mix together 1 tablespoon ground flaxseed + 3 tablespoons of water and let sit for 5 minutes. As written, this recipe calls for 2 eggs, so you would need 2 tablespoons ground flaxseed + 6 tablespoons of water.
Oil: If you enjoy the flavor of coconut, use unrefined coconut oil for a slight nutty sweetness. Otherwise, refined coconut oil keeps the muffins moist and is essentially flavorless. If you don't have coconut oil you can use canola oil, vegetable oil, or even melted and cooled unsalted butter.
Frozen Blueberries: If using frozen blueberries add them to the batter still frozen.
Storage: Store the cooled muffins in an airtight container in the refrigerator for up to 5 days or freeze the muffins for up to 3 months.
Nutrition
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.
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These are so delicious!! I used olive oil and replaced a measure of the flour with rolled or quick oats. Came out great each time and I feel good giving them to my baby. Thank you so much.
Thank you for sharing, B! If you could share how much flour you replaced with oats that would be helpful for others to know. I would assume about 1 cup would work well. Thanks!
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.