
These healthy blueberry muffins are a game-changer for anyone looking for a wholesome breakfast or snack option without sacrificing flavor. Made entirely with whole wheat flour and naturally sweetened with honey and applesauce, they bring a wonderful balance of nutty, floral, and fruity notes that truly stand out. Perfect for busy mornings or a midday pick-me-up, these muffins are easy to whip up and deliver nourishing ingredients in every bite.
I first baked these muffins on a quiet weekend and was amazed by how moist and flavorful they stayed even days later. Now they are a regular in my family’s rotation, especially handy for packed lunches or when unexpected guests arrive.
Ingredients
- White whole wheat flour: a lighter whole grain flour that adds nuttiness and nutrition while keeping muffins tender. Choose King Arthur brand for consistency or use a blend of whole wheat and all-purpose flour if unavailable
- Baking powder and baking soda: provide lift and create a soft, airy crumb
- Kosher salt: enhances sweetness and rounds out flavor
- Cinnamon: a subtle warmth that complements the blueberries and whole wheat notes
- Honey: natural sweetener and humectant to keep muffins moist over several days. Pick a quality honey like Crete’s Alfa Honey if you can
- Unsweetened applesauce: adds moisture and a touch of natural sweetness to replace butter
- Extra virgin olive oil: rich in antioxidants with a fruity, buttery flavor that deepens the taste and texture. Use a smooth variety for best results
- Milk: any type is fine including plant-based options. Greek yogurt works but yields denser muffins
- Egg: binds ingredients together for structure. Flax egg can be used but expect less fluffiness
- Fresh blueberries: the star of the show, bursting with juice and antioxidants. Frozen works too but may alter baking time and color
- Vanilla extract: rounds out and enhances the overall flavor profile
Instructions
- Sauté the Aromatics:
- This recipe does not require this step.
- Prepare the Oven and Pan:
- Preheat your oven to 375 degrees Fahrenheit and lightly grease a 12 cup muffin pan or line it with muffin liners. This ensures your muffins bake evenly and release effortlessly.
- Mix the Dry Ingredients:
- In a large bowl, whisk together one and three quarters cups of white whole wheat flour, one teaspoon of baking powder, half a teaspoon of baking soda, half a teaspoon of kosher salt, and a quarter teaspoon of cinnamon. Whisking thoroughly helps distribute the leavening agents and spices evenly for consistent flavor and rise.
- Mix the Wet Ingredients:
- In a separate bowl, combine half a cup of honey, half a cup of unsweetened applesauce, one third cup of extra virgin olive oil, and a quarter cup of milk. Whisk these together to integrate the liquids and sweeteners. Add in one large egg and one teaspoon of vanilla extract, then whisk again until fully blended.
- Combine Wet and Dry Ingredients:
- Pour the wet mixture into the bowl with the dry ingredients. Using a spatula, fold everything together carefully until just combined. Avoid overmixing to keep the muffins light and tender. It is okay if there are still some small lumps in the batter.
- Fold in the Blueberries:
- Gently fold in one and a half cups of fresh blueberries using your spatula. Then allow the batter to rest for twenty minutes at room temperature. This resting time hydrates the flour, improves the texture, and intensifies the flavor.
- Divide the Batter into the Pan:
- Spoon or pour the muffin batter evenly into the prepared muffin cups, filling each about three quarters full. Even distribution helps all muffins bake uniformly.
- Bake the Muffins:
- Place the pan in the oven and bake for about twenty two minutes or until a toothpick inserted into the center comes out clean. This time may vary slightly depending on your oven and whether you used fresh or frozen blueberries.
- Cool Completely:
- Let the muffins cool in the pan for ten minutes to firm up, then carefully transfer them to a wire rack to cool fully. Running a butter knife around the edges can help release any that stick to the pan.
- Serve or Store:
- Enjoy the muffins fresh or store them in an airtight container at room temperature for up to four days. For longer storage, freeze in a freezer safe bag or container for up to three months. Thaw at room temperature before serving.

My favorite ingredient in these muffins is definitely the white whole wheat flour. It lends a wonderful nutty flavor and keeps the crumb light without the heaviness that sometimes comes with whole wheat baking. I remember baking a batch for a family brunch, and everyone was surprised these were made with 100 percent whole wheat. It felt great to share something so healthy that tasted this good.
Storage Tips
Store these muffins at room temperature in a sealed container if you plan to eat them within four days. For longer storage, let them cool completely and freeze in a single layer before transferring to a freezer bag. This prevents them from sticking together. When ready to eat, thaw at room temperature or warm gently in the oven for a few minutes.
Ingredient Substitutions
If you do not have white whole wheat flour, try blending half whole wheat flour with half all purpose flour. Unsweetened pumpkin puree can replace applesauce for a subtle seasonal twist. You can swap the milk for any plant based milk you like such as almond or oat milk. Use frozen blueberries but add a couple of extra minutes to baking time and expect a slightly bluer colored batter.
Serving Suggestions
Enjoy these muffins plain with your morning coffee or tea. They also pair wonderfully with a spread of natural peanut butter or almond butter. A small bowl of fresh fruit or yogurt on the side makes for a balanced breakfast or snack.

These whole wheat blueberry muffins are an easy, nourishing bake that stores and freezes well. They make a great grab and go breakfast or snack for the whole family.
Common Questions About Recipes
- → What flour is best for these muffins?
White whole wheat flour is recommended for a lighter texture and nutty flavor, but a blend with regular whole wheat can work too.
- → Can I substitute the sweetener?
Honey provides moisture and natural sweetness, but maple syrup or agave can be used as alternatives with slight flavor changes.
- → How can I keep the muffins moist without butter?
Unsweetened applesauce adds moisture and tenderness, replacing the need for butter while keeping the muffins light.
- → Is it better to use fresh or frozen blueberries?
Fresh blueberries are ideal for best flavor and color, though frozen can be used with an adjusted baking time and may turn the batter blueish.
- → How should I store these muffins for freshness?
Store at room temperature in an airtight container for up to 4 days or freeze for up to 3 months, thawing before serving.
- → What role does extra-virgin olive oil play in this preparation?
It adds a subtle fruity richness and antioxidants while being less processed than other oils, enhancing the overall flavor.