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You’ll never believe that these amazing Whole Wheat Blueberry Muffins are made with 100% whole wheat. Flavored with lemon zest, these low-sugar blueberry muffins are an easy recipe the whole family will love.

Two whole wheat blueberry muffins stacked on top of each other.
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These fluffy whole wheat blueberry muffins will be your new favorite breakfast or snack.

Looking for other muffin recipes? Check out our Chocolate Zucchini Muffins and Healthy Banana Chocolate Chip Muffins. And Frozen Berry Cake is always a tasty recipe.

How to make Whole Wheat Blueberry Muffins

*I’ll walk you through it here with some photos and tips, and you’ll also find a printable recipe card at the bottom of the post with exact measurements, etc. You can also click “jump to recipe” to skip down.

Grab a medium microwave-safe bowl and melt the butter in the microwave. Let it cool slightly, and then mix in the sugar. Next up, add the egg and almond extract and whisk to combine.

Mix the blueberries with 1 tsp of flour and the lemon zest in a small mixing bowl. Stir gently to coat.

In the bowl with the butter and egg mixture, combine whole wheat flour, salt, baking powder, baking soda, and cinnamon. Give it a few stirs and then mix in the buttermilk. Whisk everything gently until about half-mixed. You’ll see lumps and some unincorporated flour.

two photos showing the process of combining ingredients.

Add the floured blueberries and gently fold them into the mixture with a silicone spatula. Allow the batter to sit for 10 minutes.

Place muffin liners into muffin tins and fill the liners to the top. Bake for 18 minutes or until a toothpick inserted in the center comes out clean.

Put the tins on a wire cooling rack for about 15 minutes, then remove them and let them cool completely before storing them in an air-tight container.

two photos showing the process of making whole grain blueberry muffins.

Frequently Asked Questions

Can I use frozen blueberries in this recipe?

Yes, you sure can! Just make sure you don’t defrost the frozen berries first or you’ll have some lovely purple muffins. Related: How to Freeze Blueberries

Can I use all-purpose flour instead of whole wheat?

Absolutely! You can use all-purpose flour in a direct substitution in this recipe. You’ll want to reduce the baking powder to 1 tsp. There is no need to adjust any of the other ingredients.

Can I use non-dairy milk instead of buttermilk?

Sure thing! Grab your favorite non-dairy milk and stir in 2 tsp of lemon juice or white vinegar. Let it sit for 5 minutes, and you now have dairy-free buttermilk.

Can I use oil instead of butter?

Yes, you can. I think the butter adds a delicious flavor, but feel free to sub in 1/2 cup of your favorite neutral-flavored oil.

Can I make these into mini muffins?

I have not tried it myself, so my best guess is that the baking time will be ~10-15 minutes. Make sure you use the toothpick test to check for doneness.

Can I make these into jumbo muffins?

I have not tried it myself, so my best guess is that the baking time will be ~22-25 minutes. Make sure you use the toothpick test to check for doneness.

How to Store and REheat

Storing Leftovers: Allow the muffins to fully cool before storing them in an air-tight container at room temperature for 2-3 days.

Reheating Leftovers: These whole wheat blueberry muffins are great at room temperature, but they’re also delicious if you like them warmed up. Zap one in the microwave for 10-15 seconds.

Freezing Leftovers: Allow the muffins to fully cool before placing them on a baking sheet or plate. Freeze for 4-5 hours and then wrap each individual muffin in foil or plastic wrap and then transfer to a freezer-safe bag.

Pro Tips/Recipe Notes:

  • Make sure that you spoon and level the flour into the measuring cups instead of scooping the measuring cup directly into the flour. This prevents the flour from being overly compacted, which results in a batter that is overly dry.
  • If using all-purpose flour, reduce the baking powder to 1 tsp.
  • This recipe uses a lot of baking powder to help get a fluffy end product. Make sure you use aluminum-free baking powder to avoid a chemical taste.
  • No buttermilk? Add 2 tsp of white vinegar to your milk of choice, stir, and let sit for 10 minutes.
  • If you love a crunchy muffin top, sprinkle raw or turbinado sugar on top just prior to baking.
  • If you do use buttermilk, save the extras for future batches. Learn more about it in this post on freezing buttermilk.
  • Top the muffins with Blueberry Freezer Jam for an epic blueberry-fest.
honey being drizzled over a whole wheat blueberry muffin

WEIGHT WATCHERS POINTS

One serving has 3 WW Freestyle SmartPoints.

5 from 10 ratings

Whole Wheat Blueberry Muffins

Prep: 15 minutes
Cook: 18 minutes
Total: 33 minutes
Two whole wheat blueberry muffins stacked on top of each other.
You'll never believe that these amazing whole wheat blueberry muffins are made with 100% whole wheat. Flavored with lemon zest, these low-sugar blueberry muffins are an easy recipe the whole family will love.

Ingredients 

Instructions 

  • Preheat oven to 400˚F.
  • Place muffin liners in a muffin tin or spray thoroughly with cooking spray.
  • In a microwave-proof bowl, melt butter. Allow it to cool slightly.
    1/2 cup butter, room temperature
  • Mix in the sugar and whisk to combine.
    1/3 cup sugar
  • Add the egg, almond and vanilla extract. Whisk.
    1 egg, 1/2 tsp almond extract, 1 tsp pure vanilla extract
  • Combine blueberries,1 tsp of flour, and lemon zest in a mixing bowl and stir gently to coat the blueberries.
    1 1/2 cups fresh blueberries, 1 tbsp lemon zest
  • In the bowl with the butter and egg mixture, combine whole wheat flour, salt, baking powder, baking soda, and cinnamon. Stir a few times.
    2 cups whole wheat pastry flour, 1 tsp salt, 2 tbsp baking powder, alumnimum-free, 1 tsp baking soda, 1 tsp cinnamon
  • Mix in the buttermilk to the mixture. Whisk gently until about half mixed. You'll see lumps and some unincorporated flour.
    1 cup buttermilk
  • Add the floured blueberries and gently fold it into the mixture with a silicone spatula. Allow to sit for 10 minutes.
  • Fill the muffin liners to the top. Bake 18 minutes or until a toothpick inserted in the center comes out clean.
  • Put the tins on a wire cooling rack for about 15 minutes, then remove and let cool completely before storing in an air-tight container.

Notes

  1. Make sure that you spoon and level the flour into the measuring cups instead of scooping the measuring cup directly into the flour. This prevents the flour from being overly compacted, which results in a batter that is overly dry.
  2. Make sure you use aluminum-free baking powder to avoid a chemical taste.
  3. If using frozen blueberries, do not defrost the berries prior to adding them to the batter.
  4. Sprinkle a bit of raw sugar or turbinado sugar on top just prior to baking for a nice crunchy top.
  5. Using all-purpose flour? Reduce the baking powder to 1 tsp.

Nutrition

Serving: 1muffinCalories: 127kcalCarbohydrates: 16gProtein: 2gFat: 6gSaturated Fat: 3gCholesterol: 24mgSodium: 175mgPotassium: 213mgFiber: 1gSugar: 5gVitamin A: 200IUVitamin C: 1.7mgCalcium: 83mgIron: 0.7mg

Nutrition information is automatically calculated, so should only be used as an approximation.

Additional Info

Course: Baked Goods
Cuisine: American
Tried this recipe?Mention @sustainablecooks or tag #sustainablecooks!

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About Sarah

Helping you serve up budget-friendly sustainable recipes with a side of balanced living.
Come for the food. Stay for the snark.

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20 Comments

    1. I’d love to help you troubleshoot where it might have gone wrong. Without being in the kitchen with you, it’s hard to say what might have happened. Are you used to whole wheat products? Perhaps the taste of whole wheat isn’t your cup of tea?

      That being said, your email address is coming from a spam account, so I’m not sure how seriously I should be taking your comment. I’m more than willing to help real readers who are actually making my recipes, instead of bored trolls.

  1. These sound soooo yummy! My kids have been complaining that we haven’t made anything for awhile. This will be the perfect recipe!5 stars

  2. I received my grain mill last weekend. A neighbor had given me some fresh stone ground whole wheat pancake mix. I have never tasted anything so fantastic. we always eat whole wheat in our house, and it mostly tastes bitter to me. Not this, it was almost sweet and sooo delicious. That sent me on the quest for a grain mill. I made these muffins using my freshly ground ww flour and they are pure heaven! Honestly people, this is the way to go!5 stars

    1. Deb, welcome to the world of flour making!! It’s so awesome, isn’t it? What brand did you get?

      So glad you loved the muffins. It reminds me to make a batch soon! 🙂

  3. Hi,

    Egg isn’t in the ingredient list.  It sounds like only one egg from reading through the info, but wanted to make sure.

    Thanks!5 stars

  4. Hi Sarah, So glad to have found your website. (I heard you on chopped podcast.) Love what you’re all about and I can sooo relate to so much of what you said. Especially about my readers not liking my desserts because they are too healthy. LOL! I was like “Yes Totally!” out loud to my car radio. Also, love these muffins. We have a billion frozen blueberries from picking this summer. I’ll have to pass this recipe on to my 4th grader to make. She has gotten into cooking/baking lately and wants snack recipes. Anywhoo, glad to know about your blog and follow along now.5 stars

    1. Hi Katie! Thanks for coming over from Chopped! That dessert comment still makes me laugh to this day.

      I have a fourth grader who is not into baking. I need to make that happen; thanks for the motivation!!

  5. Thanks for the freezer tip, Sarah, I’ll have to try that. I love the touch of almond with the earthiness of the whole wheat flour. Sounds great.5 stars

  6. I’m loving how often you post now that you work at home full time. I’ve been trying to send you a pic of my hubs’ recent score at a restore but it won’t send. You’ll be jealous. A mini cast iron stove for 60 bucks. It’s in storage for our retirement home. BTW your boys are adorable.5 stars

    1. I wish it were more often, but the little stinker won’t nap longer than 20-25 minutes. I’d love to post four times a week!

      I’m so jealous of that restore find. WOW!!!