Whole Wheat Blueberry Muffins

100% Whole Wheat Blueberry Muffins the way they should be: moist, fruity, and sweetened just-so. Make a double batch and freeze these for a quick breakfast or lunchbox treat. 

whole wheat blueberry muffins

Who loves to batch-cook muffins?

Let me rephrase that: Who loves to have a stash of delicious, healthy, homemade, muffins in the freezer?

Here’s a nourishing whole grain recipe, famously bursting with fat fresh blueberries, that you can serve your kids with confidence, and tuck into the freezer for quick breakfasts on busy mornings.

basket of whole wheat blueberry muffins

Kids Love Whole Wheat Blueberry Muffins

You won’t have to beg and cajole your kids eat these classic muffins. The taste of these muffins compares to that of any blueberry muffin, sweet and moist and simple. As far as most kids are concerned, that equals “yummy.”

Wondering how they’ll do with 100% whole wheat flour? If you think they might shy away from the whole grains, choose white whole wheat flour for muffins that turn out fluffy and delicate, with fiber and vitamins that compare well to darker “red” wheat flour.

Using “regular” whole wheat flour works just fine with these muffins, too, but you can expect a slightly darker color, and more rustic texture.

homemade blueberry muffins

What Makes These Whole Wheat Blueberry Muffins Healthy?

Bakers walk a fine line between making healthy fruit muffins and making, well, cake. Our honest assessment of the majority of muffin recipes out there in ye olde internet world is that they have way too much sugar for a breakfast food or everyday snack. One cup of sugar (or honey or maple syrup) makes a muffin just as sweet as a pan of brownies or a batch of cookies.

(Side note: we don’t object to cookies or brownies outright. We just save the really sweet stuff for dessert.)

When it comes to a breakfast staple like muffins, we have demands. Here’s what we look for:

  1. Somewhere around 1/4 cup of added sweeteners, maximum. Whether that’s honey, sugar, OR maple syrup.
  2. Whole grains. The higher percentage of whole grains, the better.
  3. Fruits or veggies–for nutrition, and for the message they send: that fruits and veggies belong at every meal.
  4. A flavor that kids swoon over.

This recipe hits all four notes, which is why we love it so. And we’re pretty sure you’ll love it, too!

homemade blueberry muffins

Links for Muffin-Lovers

Healthy muffins is a thing we do. Like a lot. Check out a few of our most popular muffin recipes below:

Power-Packed Fruit and Veggie Muffins

Sweet Spinach Muffins

Healthy Chunky Monkey Muffins

whole wheat blueberry muffins


Whole Wheat Blueberry Muffins | Healthy Ideas and Recipes for Kids

Whole Wheat Blueberry Muffins

Whole Wheat Blueberry Muffins
Serves: 12 Muffins
Serving Size = 1 muffin
Prep Time: 10 m
Cook Time: 25 m


  • 1 1/2 cup – flour, whole wheat
  • 1 teaspoon – baking powder
  • 1/2 teaspoon – baking soda
  • 1/3 cup – butter, unsalted
  • 1/4 cup – sugar
  • 2 large – egg
  • 2 teaspoon – vanilla extract
  • 1/2 cup – yogurt, plain
  • 1 cup – blueberries
  • 12 standard – cupcake liners


  1. Preheat oven to 350 degrees F.
  2. In a large mixing bowl, stir together flour, sugar, baking soda, and baking powder.
  3. Make a well in the dry ingredients and add eggs, vanilla, yogurt, and melted butter. Stir until wet and dry ingredients are just combined (don't over-mix.)
  4. Gently fold in blueberries.
  5. Line a muffin tin with paper liners, or lightly grease the tin with butter. Spoon batter evenly into tin.
  6. Bake on middle rack for 20-25 minutes, or until the tops are a light golden brown and a toothpick inserted into the middle muffin comes out clean.
*Fresh or frozen blueberries can be used. Coat frozen blueberries with 1 tablespoon of flour to prevent berries from bleeding.

Nutrition Facts

  • Nutrition per serving % daily value
  • Calories: 139 7%
  • Fat: 6 g 9%
  • Carb: 17 g 6%
  • Fiber: 1 g 4%
  • Protein: 3 g 6%
  • Sugar: 6 g
written by
Natalie Monson

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Allison says:

Any suggestions on how to reduce the sugar and butter in the recipe to make them even healthier but still tasty? Also is this recipe for 12 muffins or 24?

Natalie Monson says:

This recipe is for 24 muffins. You can experiment by adding more applesauce and less butter for sure! THe sugar you would just the reduce amount – if you experiment with it, let us know how they turn out!

Preeti says:

hi , what can i use instead of applesauce, if i dont have applesauce readily available

Preeti= you could actually use any fruit that is blended. Even blended fruit found in baby food jars would work.

Sats says:

absolutely delicious.!!

Casey says:

I realize that buttermilk has a very distinct flavor but if I can’t find it over here (we are stationed in Italy and grocery availability is, well, Italian….) what would you recommend???

Natalie Monson says:

You can make your own buttermilk using vinegar or lemon juice. Just add 1 Tablespoon of vinegar or lemon juice to every cup of milk and let it sit for 10 minutes. SO easy!

I just made these. They smell SOOO good!

Natalie says:

No it isn’t. This method just produces a more tender fluffy consistency. You can definitely soften the butter and add it in. Good luck!

Jennifer says:

Hi, I was wondering if it is totally necessary for the butter to be cold? I don’t have a food processor so I was wondering how I would mix this by hand? Could I soften the butter a bit to make mixing easier? Or would a hand mixer work? These look great by the way!

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Natalie says:

Sorry about that! Yes, add to the wet ingredients.

Natalie says:

These are full size muffins. If you make mini muffins I would probably cut the cooking time almost in half.

Natalie says:

I haven’t tried it with coconut palm sugar, but I think it would probably work great!

Aimee says:

I followed exactly and mine came out very floury tasting. Almost a rubbery texture. I feel like there wasn’t enough wet to go with do much dry.

Audi says:

The pictures and the actual instructions are so off. Even the oven temps are different.

Audi says:

Where is the applesauce in the instructions? I added it to the wet ingredients. Hope it works!

Jennifer says:

I was also curious about adding coconut sugar. Would that, maple syrup, work?

Jessica says:

Did you make full size or mini muffins in this recipe? If I were to make mini muffins do you know how the cooking time would change? Thanks in advance!

Stacy says:

Hi! Would coconut palm sugar work instead of sugar? Thanks.

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Natalie says:

So glad you liked them!

Laura says:

Just made these muffins yesterday and my husband, son, and I LOVE them!!! Best muffins I’ve had in a long time. I think the cooking them at a higher heat for the first part helped to make them crunchy on the outside and perfectly soft on the inside!

Blake says:

Those muffins look so yummy. I love blueberries so much, so I know I will definitely like the muffins. Thanks for the recipe. What a healthy recipe.

david says:


Lauren says:

Thanks! I appreciate the response.

Natalie says:

It would be a 1:1 ratio. So for every cup of whole wheat flour you would use 1 cup of white whole wheat flour.

Lauren says:

Nice! Do you know what the right proportions might be for White Whole Wheat flour? I bought a bag of it and would love to use it.

Healthy, Happy Eaters.
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Join over 100k + subscribers and get family-friendly recipes, picky-eater strategies, lunch-packing tips and more, delivered each week to your inbox.