
These healthy blueberry muffins use honey and whole wheat flour to replace refined sugar and white flour, creating a muffin that is both nutritious and delicious. The combination of nutty whole wheat and fresh blueberries makes these muffins fluffy and flavorful while keeping them wholesome enough for breakfast or a snack anytime. They are easy to prepare and perfect for those who want a better-for-you treat without sacrificing taste.
I began baking these muffins during the busy mornings when I needed quick and healthy snacks. Now, they are a favorite in our household and often requested for weekend breakfasts and to pack along for work.
Ingredients
- White whole wheat flour: This whole grain flour offers a nutty taste and lighter texture compared to traditional whole wheat. King Arthur brand is a reliable option but pastry flour can also work well.
- Baking powder and baking soda: These provide the lift and fluffiness ensuring soft muffins.
- Kosher salt: Enhances the flavors and balances the sweetness.
- Cinnamon: Just a touch gives a warm subtle complexity that pairs beautifully with blueberries.
- Honey: A natural sweetener and humectant that keeps muffins moist. High-quality honey such as Alfa Honey adds floral notes.
- Unsweetened applesauce: Adds moisture without the fat of butter and contributes gentle natural sweetness.
- Extra virgin olive oil: Use a buttery, smooth variety like Nocellara to infuse a delicate fruity flavor.
- Milk: Any milk works here including plant-based alternatives for a dairy-free option. Greek yogurt can be used but yields denser muffins.
- Egg: Acts as a binding agent providing structure and elasticity.
- Fresh blueberries: Use fresh for best texture and taste. Frozen can be used but baking time will need to be adjusted slightly.
- Vanilla extract: Enhances and rounds out the overall flavor.
Instructions
- Get ready:
- Preheat your oven to 375 degrees Fahrenheit. Lightly grease a 12-cup muffin pan or line it with cupcake liners to prevent sticking.
- Mix the dry ingredients:
- In a large bowl, whisk together one and three quarters cups of white whole wheat flour, one teaspoon baking powder, half a teaspoon baking soda, half a teaspoon kosher salt, and a quarter teaspoon cinnamon. This combination builds the muffin's foundation with balanced leavening and spice.
- Mix the wet ingredients:
- In a separate bowl, combine half a cup honey, half a cup unsweetened applesauce, one-third cup extra virgin olive oil, and one-quarter cup milk. Whisk them until fully blended. Add one large egg and one teaspoon vanilla extract and whisk again until smooth and uniform.
- Combine wet and dry:
- Pour the wet mixture into the dry ingredients. Using a rubber spatula fold gently until just combined. It is important not to overmix; a few lumps are fine and will help maintain a tender crumb.
- Fold in the blueberries:
- Add one and a half cups fresh blueberries to the batter and fold in carefully with the spatula to avoid bursting the berries. Let the batter rest for twenty minutes to allow the flour to fully hydrate, which improves the texture.
- Divide the batter:
- Spoon the batter into your prepared muffin pan, filling each cup about three quarters full to allow room for rising.
- Bake:
- Place the pan in the preheated oven and bake for about twenty-two minutes or until a toothpick inserted in the center comes out clean. This step ensures the muffins are perfectly cooked through without drying out.
- Cool and serve:
- Allow the muffins to cool in the pan for ten minutes to set their shape. Then transfer them to a wire rack to cool completely. If some muffins stick, gently run a butter knife around the edges to free them.

My favorite part of this recipe is how the gentle cinnamon and honey transform simple ingredients into something comforting and special. I still remember sharing these muffins on a chilly weekend morning with my family and seeing everyone go back for seconds.
Storage Tips
Store these muffins at room temperature in an airtight container, where they will remain soft and moist for up to four days. When freezing, use a freezer-safe container or bag to preserve freshness. Thaw at room temperature or briefly warm in the oven or microwave before serving for the best experience.
Ingredient Substitutions
If white whole wheat flour is unavailable, you can substitute half with all-purpose flour to lighten the texture while still gaining some whole grain benefits. Use maple syrup instead of honey for a different natural sweetness and a hint of caramel flavor. Unsweetened Greek yogurt can replace milk for a tangier taste, but expect a denser muffin. You can try coconut oil in place of olive oil if you prefer a milder, more neutral fat profile.
Serving Suggestions
These muffins are wonderful on their own or paired with a pat of butter and a drizzle of honey or jam. Fresh fruit or a cup of coffee or tea complements them beautifully. They also make a convenient breakfast on the go or midday snack to keep energy steady.

Wholesome and simple, these blueberry muffins are perfect for quick breakfasts or snacks. Enjoy them warm or freeze for later.
Your Recipe Questions Answered
- → What type of flour is best for these muffins?
100% white whole wheat flour is recommended for a lighter color and nutty flavor, but a mix with all-purpose flour can be used.
- → Can frozen blueberries be used?
Yes, but allow extra baking time and expect a slight color change in the batter from the frozen berries.
- → What sweetener is included in the batter?
Honey is used as a natural sweetener, providing moisture and a gentle floral sweetness.
- → Is applesauce necessary in the mixture?
Applesauce adds moisture and replaces butter for a tender texture without extra fat.
- → How should these muffins be stored?
Keep at room temperature in an airtight container up to 4 days or freeze for up to 3 months.
- → Can dairy-free milk be used?
Yes, plant-based milks work well and can substitute dairy milk without altering texture significantly.