Want healthy meals your kids will love?

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


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3.4 from 77 votes

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. 

Prep Time10 minutes
Cook Time25 minutes
Total Time35 minutes
Course: Breakfast
Cuisine: American
Servings: 12 1 muffin
Calories: 140kcal



  • Preheat oven to 350 degrees F.
  • In a large mixing bowl, stir together flour, sugar, baking soda, and baking powder.
  • Make a well in the dry ingredients and add eggs, vanilla, yogurt, milk, and melted butter. Stir until wet and dry ingredients are just combined (don't over-mix.)
  • Gently fold in blueberries.
  • Line a muffin tin with paper liners, or lightly grease the tin with butter. Spoon batter evenly into tin.
  • 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.


Calories: 140kcal | Carbohydrates: 18g | Protein: 4g | Fat: 7g | Saturated Fat: 4g | Cholesterol: 45mg | Sodium: 73mg | Fiber: 2g | Sugar: 6g
Keyword : Whole Wheat Blueberry Muffins


Whole Wheat Blueberry Muffins | Healthy Ideas and Recipes for Kids

Natalie Monson

I'm a registered dietitian, mom of 4, avid lover of food and strong promoter of healthy habits. Here you will find lots of delicious recipes full of fruits and veggies, tips for getting your kids to eat better and become intuitive eaters and lots of resources for feeding your family.

Learn More about Natalie
3.41 from 77 votes (73 ratings without comment)

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Recipe Rating


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.

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.

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!

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!

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.

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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!

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???

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!

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?

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!

2 stars
I feel like an ingredient got left out when the recipe was updated at some point. The batter has the consistency of cookie dough, not muffin batter. I see older comments reference applesauce and buttermilk, but neither are in the current recipe. I added milk until the consistency seemed right and they came out OK. More light and airy than dense and moist.

Hi Erika! We have indeed updated this recipe, and the ingredients are correct as written. You’re right that the batter is quite thick, but I promise you the muffins cook up light and fluffy, even without adding extra liquid. (This recipe is a staple in our home… I stand behind it fully 🙂 ) I’m glad your batch turned out, too!

Hi Joan, sorry about that! We’re having a technical issue with our recipe plugin today. We’re working on fixing it now. Thanks for your patience!

hi! is the recipe good to go as stated above? and would using frozen blueberries work?

looking forward to trying it out!!
thank you!!!

Hi Brigitte, yes the recipe is good to go. I can personally attest to it. 🙂 Frozen blueberries do work, although they might dye the batter a bit blue, in my experience.

5 stars
Your blog is filled with unique good articles! I was impressed how well you express your thoughts.

Hi, I would like to know that can I use frozen blueberries, coconut oil and flaxseed/water mixture instead of fresh blueberries, butter and eggs?

Hi Jas, I haven’t tried those substitutions myself but I would expect them all to work just fine in this recipe.

When was I supposed to add the milk? It doesn’t say anything in instructions. Am I not seeing it? I’ve reread numerous times.


Hi Belinda, thanks for pointing out that omission! Add the milk to the “well” along with the rest of the wet ingredients. I updated the recipe.

Any recommendations for a sugar substitute? Would a banana and some honey and/or maple syrup work (similar to your healthy spinach muffins where there is no added sugar)?