These whole wheat blueberry muffins are filled with whole grains and bursting with fresh fruit. These blueberry muffins make a great side for breakfast or a quick snack!

Two Whole Wheat Blueberry Muffins sitting in front of a pan of muffins.

It’s official, I’ve kind of become obsessed with blueberries. After making this blueberry lemon bread, I’ve been eating them any way I can. They’ve been making their way into my yogurt, salads, and now these muffins. I seriously can’t get enough of them!

I love how soft and juicy blueberries become when they’re baked, which is why I wanted to use some more in these whole wheat blueberry muffins. These muffins are soft, moist, and bursting with fresh blueberries.

The best part? They’re slightly sweet and much healthier than your average muffin too, clocking in at right under 150 calories a muffin. These are perfect to have with breakfast or as a snack!

Another thing I love about these muffins is that they’re lightly sweetened with honey and coconut sugar. Have you tried it before? I love baking with it when I can!  

So, if you’re kind of a little obsessed with blueberries lately like me, then give these sweet little blueberry muffins a try. 

A stack of three whole wheat blueberry muffins. The top muffin has a bite missing.

Ingredients in This Recipe 

In addition to being made with whole wheat flour, these are also dairy-free blueberry muffins (provided you use non-dairy milk). Win-win! Here’s an overview of the ingredients you’ll need to make this recipe: 

  • Flour: These blueberry muffins from scratch are made with half all-purpose flour and half whole wheat flour. The combination of the two helps to keep the texture of these muffins light. 
  • Baking powder: Helps the muffins rise and prevents them from being too dense. 
  • Salt: Enhances the flavor of the batter.
  • Milk: Use non-dairy milk to keep these whole wheat muffins dairy-free. 
  • Oil: I made these blueberry muffins with oil to keep them dairy-free, and also to make them super moist. 
  • Egg: To bind everything together. I suggest using a room temperature egg too.
  • Honey: Sweetens the batter. I don’t recommend substituting it with maple syrup as honey is much thicker than maple syrup. 
  • Coconut sugar: Coconut sugar is an unrefined sugar that has a nice caramelized flavor and has a lower glycemic index than regular sugar. 
  • Vanilla extract: Use pure vanilla extract for the best flavor. 
  • Blueberries: You’ll need to toss the berries with some flour to prevent them from sinking to the bottom of the muffins. 

How to Make Whole Wheat Blueberry Muffins 

In a large bowl, whisk together the dry ingredients. In another bowl, whisk together the wet. Combine the two, then fold in the berries. 

You’ll need to toss the blueberries in 1 tablespoon of flour, otherwise they’ll sink to the bottom of the muffins as they bake. 

Fill each cavity of a 12-cup muffin pan two-thirds full, then bake the muffins until done. 

Overhead view of three healthy blueberry muffins. One muffin has been torn in half.

Can I Make This Recipe with Just Whole Wheat Flour?

No, I would not suggest using trying to use only whole wheat flour for this recipe, otherwise, you might end up with muffins that are much denser.

Can I Substitute the Coconut Sugar? 

Yes! If you don’t have coconut sugar, no worries. You can substitute granulated sugar or brown sugar for the coconut sugar instead.

Baking Tips

  • Make sure the milk and egg are both room temperature before making this healthy blueberry muffin recipe. This is especially important if you’re also using coconut oil, as coconut oil will harden when it comes in contact with cold ingredients. 
  • You’re welcome to use fresh or frozen blueberries. If using frozen, add them to the batter straight from the freezer and bake the muffins for a couple extra minutes. 
  • These muffins freeze and reheat beautifully, so consider making a big batch for later. 

More Easy Muffin Recipes to Try!

Whole Wheat Blueberry Muffins

4.75 from 4 ratings
Prep Time: 10 minutes
Cook Time: 15 minutes
Total Time: 25 minutes
These whole wheat blueberry muffins are filled with whole grains and bursting with fresh fruit. These blueberry muffins make a great side for breakfast or a quick snack!


Servings: 12 muffins
  • 3/4 cup all purpose flour (spoon and level to measure)
  • 3/4 cup whole wheat flour
  • 2 tsp. baking powder
  • 1/4 tsp. salt
  • 1/2 cup milk (any kind)
  • 1/4 cup oil (coconut, vegetable, or canola work well)
  • 1 egg
  • 1/4 cup honey
  • 1/4 cup coconut sugar*
  • 1 tsp. vanilla extract
  • 1 cup blueberries washed and patted dry + 1 tbsp. all purpose flour


  • Preheat oven to 350 degrees F. Spray a 12-count muffin pan with cooking spray and set aside.
  • In a small bowl, mix the blueberries and tablespoon of flour together and set aside.
  • In a large bowl, whisk together both flours, baking powder, and salt.
  • In a separate bowl, whisk together the milk, oil, egg, honey, coconut sugar, and vanilla.
  • Combine the wet and dry ingredients, mixing until just combined. Make sure not to over mix the batter.
  • Gently fold the blueberries into the batter.
  • Scoop out the batter evenly into each muffin tin (about two-thirds of the way full).
  • Bake for 15-18 minutes, remove from oven and allow to cool in pan for about 10 minutes then transfer to wire rack to cool completely.


Coconut sugar: The coconut sugar can be substituted with granulated sugar or brown sugar.
Storage instructions: Store cooled muffins in an airtight container on the counter for 3-4 days, in the refrigerator for up to one week, or freeze for up to two months.
Cuisine: American
Course: Breakfast
Author: Danielle Rye
Serving: 1g, Calories: 144kcal, Carbohydrates: 22.2g, Protein: 2.4g, Fat: 5.4g, Fiber: 1.6g, Sugar: 10.8g
Did you make this recipe?Mention @livewellbakeoften on Instagram or tag #livewellbakeoften.

Adapted from Whole Wheat Strawberry Muffins (originally adapted from All Recipes).