The best blueberry muffin recipe that’s wholesome and delicious! These whole wheat blueberry muffins are so easy and quick to make using frozen blueberries, and 100% whole wheat flour. I love this blueberry muffin recipe and our children beg for them for breakfast!

blueberry muffin recipe with whole wheat flour

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For more blueberry muffin recipes try our blueberry muffins recipe from fresh blueberries and all-purpose flour. We prefer the more healthy blueberry muffins from whole wheat flour and its bran. I buy my whole grains from Azure including this Organic cane sugar for these blueberry muffins.

Whole Wheat Blueberry Muffins:

These small domed, quick bread cakes are incredible! I found this blueberry muffin recipe in an old-fashioned cookbook written by a farmer’s family back in 1976. The original recipe called for sifted flour, which I adapted by adjusting the liquid to use freshly ground whole wheat flour.  Of course, I added more blueberries and cut back on the sugar.

I love everything about these homemade blueberry muffins they are still plenty sweet, bursting with blueberries, and full of whole grains. The first time I made them our children were asking me to make them the next day, I then came to realize it was a keeper because it was in high demand with no leftovers! I like to serve these in the morning for breakfast with some softened butter and call it a nutritious meal (no complaints on whole wheat flour!) So, I call it a win, win.

blueberry muffins in a muffin pan

Best Kind of Blueberries To Use:

I typically use frozen blueberries that you can buy from Azure Standard, they carry organic blueberries or the wild blueberry variety, which is super wholesome. However, any blueberries can be used in muffins including 1/2 cup of dried blueberries or 2 cups of fresh blueberries when in season. Frozen blueberries are the best option for year-round blueberries and I love that Azure standard blueberries freeze very well.

Blueberry Muffin Ingredients:

  • Whole Wheat Flour- soft white wheat berries are what I used to make the whole wheat flour here. You want to use low-gluten pastry flour for quick bread like muffins. If you wish to use regular all-purpose flour or gluten-free flour blend simply use 2 cups of flour and omit the water.
  • Leavening- baking powder helps the dough rise when baking. Baking soda is pure sodium bicarbonate and is much stronger so use baking powder for this recipe.
  • Sugar- I use organic cane sugar that works just like regular granulated sugar but unrefined. For a crackly top sprinkle some on top of the muffins.
  • Salt- we grind our own coarse sea salt at home using a spice grinder.
  • Eggs- you only need one egg and slightly beat it with a fork before adding it to the batter. Eggs will help bind the muffins together, for an egg substitute make a flax egg by combining one tablespoon of flaxseed meal and three tablespoons of water and allow to sit for about 5 minutes (this is equivalent to one egg.)
  • Buttermilk- the original recipe called for 1/2 cup of milk, however, I only had buttermilk on hand and had to add water to adjust the thickness. The muffins came out fantastic! For dairy-free, try oat milk, unsweetened almond milk, or coconut milk.
  • Butter- melt unsalted butter for these muffins or use healthy cooking oil. I usually have sunflower oil on hand or olive oil.
  • Blueberries- fresh or frozen blueberries will work for this recipe. I tend to have frozen on hand and just add them to my muffin mix frozen when adding. I also like to reserve about 1/2 cup for the top, that’ll just dollop to make them look like they’re bursting with blueberries but that’s totally optional.

Measuring Whole Wheat Flour:

How to measure flour? I’ve learned that fluffing up the flour and spooning it into a measuring cup doesn’t quite work with freshly ground whole wheat flour. Because the germ, bran, and endosperm are present, wheat flour is fluffier in volume taking up more space in a cup. It’s best to scoop the flour directly from the canister using a measuring cup and gently shaking off any flour rather than scraping a knife across the top.

Whole Wheat Flour vs all-purpose flour? Recipes by weight always remain the same in the amount of flour you use. In grams, one cup of white flour weighs more than a cup of whole wheat flour. That is because white flour is more compact being made up mostly of the endosperm.

How To Make Blueberry Muffins:

Quick bread couldn’t be easier! This blueberry muffin mix gets layered with dry ingredients, and then wet ingredients all in one bowl! Everything gets whisked together and then scooped into a standard muffin pan.

  1. Whisk the dry ingredients together (whole wheat flour, baking powder, sugar, and salt.
  2. Add the wet ingredients (beaten egg, buttermilk, water, and melted butter.)
  3. Using a rubber spatula fold in the blueberries. Be careful not to overmix the batter, you don’t want the blueberries to bleed into the batter.
  4. Scoop the muffin batter into a non-stick muffin pan (or line the muffin cups with liners) and bake for 15-20 minutes.

How Long To Bake Blueberry Muffins? Whole wheat blueberry muffins are done when the muffins come out clean, and the centers puff out with a domed top. Quick Bread muffins are done when the internal temperature reaches 200°F-205°F. Use a good quality food thermometer and check for doneness after 20 minutes.

Easy Whole Wheat Blueberry Muffins 3-Ways:

Make a variety of muffin sizes using different muffin pans. We like the more traditional muffins using a standard muffin tin but you can go with any size!

  • For Bakery Style, blueberry muffins use this Jumbo Muffin Pan. Makes 6-7 big topped muffins.
  • Our recipe makes 11 standard-size blueberry muffins, I know a little odd but when making this recipe with heaping ingredients it fits into all 12 muffins.
  • Use a mini muffin pan to make mini blueberry muffins.

We found these to be the best wholesome blueberry muffins from scratch. A friend of ours commented “Amazing, this recipe will definitely go into my fresh-milled grain cookbook!” Leave a comment below to share your experience!

Muffin Variations:

Use your favorite recipes for blueberry muffins as a base to build your flavor profile. Here are creative ways to make different muffins using the same whole wheat batter only different add-ins;

  • Blueberry Muffins with Crumb Topping: make this streusel topping of 3 T of flour, 1/3 cup sugar, 3/4 tsp cinnamon, and 2 Tbsp butter.
  • Lemon Blueberry muffins: add 1 tsp of lemon extract to the batter and the zest of 1 lemon.
  • Banana muffins: add 1 cup of mashed bananas, only 1/2 cup of liquid, and 1 tsp of vanilla extract. Bananas can make moist muffins!
  • Pumpkin Muffins: increase the sugar to 1 cup and add 1 Tbsp of pumpkin spice seasoning, and one 15 oz can of pumpkin puree.
  • Chocolate Chip Muffins: use 1 cup of chocolate chips instead of the blueberries.

What To Serve with Blueberry Muffins:

This recipe for blueberry muffins is a favorite for breakfast with plain unsalted butter. They’re like protein cakes (from whole grain), that make a quick grab-and-go breakfast or are something scrumptious you can enjoy by the table.

  • Serve with hot tea or coffee
  • We love to slather these blueberry muffins with softened Kerry Gold butter!
  • With a side of Scrambled eggs and bacon 
  • Fresh fruits on the side
  • A bowl of oatmeal or hot cereal


How To Store Blueberry Muffins:

How long do blueberry muffins last? Freshly baked muffins can last up to a week in an airtight container. Refrigerate blueberry muffins once they cool and keep them refrigerated when storing as homemade baked goods can get moldy quickly, especially in warmer climates. You can always reheat blueberry muffins in the microwave until warm.

Can You Freeze Blueberry Muffins?

Yes! Whole Wheat blueberry muffins can be frozen after baking. Simply cool and wrap each muffin in plastic wrap then place them into a gallon-sized freezer bag and keep them frozen for up to 3 months. Pull out as many as you need. Thaw overnight in the fridge before serving.


Tips for Making an Egg Sandwich:

  1. To keep blueberries from sinking reserve 1/2 cup of frozen blueberries for dolloping over the tops. These don’t sink to the bottom but make beautiful muffin tops with bursting blueberries.
  2. Make waffles from this batter, simply cook the batter in your waffle maker.
  3. Substitute part almond flour or oatmeal flour for gluten-free options or just use a gluten-free flour blend.
  4. This is the blueberry muffin pan I own, it’s the USA pan that is non-stick.
  5. Cultured buttermilk is thick, the best substitute is sour cream or yogurt.
  6. You can also omit the buttermilk and water and use all milk, I would add 3/4 cup of milk first then add the remaining 1/4 cup to desired thickness.


More Quick Bread Recipes:

How To Make Whole Wheat Blueberry Muffins:

Whole Wheat Blueberry Muffin Recipe

Prep Time: 5 minutes
Cook Time: 20 minutes
Total Time: 25 minutes
Servings: 11 muffins
The best blueberry muffin recipe that's wholesome and delicious! These whole wheat blueberry muffins are so easy and quick to make using frozen blueberries, and 100% whole wheat flour. I love this blueberry muffin recipe and our children beg for them for breakfast!


  • 1 standard muffin pan
  • 1 mixing bowl
  • 1 Wire Whisk (to mix batter)
  • 1 rubber spatula (to fold in blueberries)





  • Whisk together the dry ingredients (wheat flour, baking powder, sugar, and salt.)
  • Add the wet ingredients (beaten egg, buttermilk, water, and melted butter) and whisk well.
  • Using a rubber spatula gently fold in the frozen blueberries.
  • Scoop batter into 11 standard muffin cups. Bake at 375°F for 20 minutes or until tops are domed-shape and golden brown.

Nutrition per serving

Serving: 1muffinCalories: 193kcalCarbohydrates: 38gProtein: 5gFat: 4gSaturated Fat: 2gPolyunsaturated Fat: 1gMonounsaturated Fat: 1gTrans Fat: 0.1gCholesterol: 22mgSodium: 126mgPotassium: 288mgFiber: 4gSugar: 17gVitamin A: 120IUVitamin C: 3mgCalcium: 90mgIron: 1mg

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