These are truly the Whole Wheat Blueberry Muffins I have ever had. Light, tender and moist, these healthy blueberry muffins are bursting with fresh blueberry flavor and are made with Greek yogurt, olive oil, and honey for a delicious breakfast or snack you can feel good about.

The Secret to this Healthy Blueberry Muffin Recipe

I find there are two things that cause muffins to be less-than-impressive—they’re either gluey (which some people like to call “moist”) or dried out. The key to a perfect muffin is achieving harmony between moistness, tenderness and airiness. 

With about 10 ingredients and two bowls you can have this delicious healthy blueberry lemon muffin recipe whipped up in about 40 minutes. That’s exactly the quick and easy type of breakfast or snack recipe we’re looking for.

These muffins have everything going for them, they’re:

  • Naturally-Sweetened. All just with the goodness of honey, no sugar added.
  • Heart-Healthy Fat. We swapped butter for olive oil here, it gives a savory note and also keeps the muffins so tender.
  • Moist and Dense. No one likes a dry muffin, the Greek yogurt keeps these muffins moist but also with a substantial texture like a bakery-style muffin. Plus it adds some protein too!
  • Bakery-Style Cupcakes at Home. To help you look like a professional baker, the cornstarch and oven temperature are two tricks of the trade to make these muffins look almost too pretty to eat.
  • Full of Flavor. They’re healthy but you would never know it! With lemon zest stirred in the batter and a crunchy turbinado sugar topping, these muffins are the ideal healthy swap.

Don’t worry, I’ve tested this recipe so many times to make sure they’re the ultimate muffin recipe that’s also nutritious. Through that process I identified different health ingredient swaps and tips that I’m sharing with you.

These muffins have the best texture and great flavor to back them up! I love that they aren’t too sweet! The turbinado lemon zest topping adds the perfect crunch! Thank you for this delicious, healthy muffin recipe!! – Abby K.

Healthy blueberry muffins in a muffin tin.


  • Whole-wheat pastry flour: such a wonderful ingredient for healthy baking! It’s great for whole-wheat tart crusts, quick breads like Sweet Potato Bread and Carrot Bread, and Chocolate Chip Walnut Cookies.
  • Cornstarch: this is key for making muffins tender! You can substitute with arrowroot starch if needed.
  • Baking powder and soda: the combination of leaveners creates a tall, stable lift.
  • Plain Greek yogurt: The acid in the dairy activates with the baking soda and helps to create a baked good that’s tender and airy. 
  • Honey: this recipe is naturally sweetened with honey. You’ll need ½ cup. I have not tested this recipe with maple syrup so I do no recommend making the swap.
  • Olive oil: instead of butter, heart-healthy olive oil is used to make these muffins nice and moist.
  • Eggs: it’s important to use eggs labeled as “large” not medium, not Jumbo, you need large eggs. A large egg, out of shell, should weight about 50 grams.
  • Lemons: this recipe uses the zest of 2 lemons. Use the zested lemons to make a lemony Dill Vinaigrette or Lemon Margarita.
  • Almond or vanilla extract: you can use either here. Vanilla is more traditional while I find the almond extract adds a delicious aroma and surprising flavor.
  • Fresh blueberries: fresh is best! I like to seek out blueberries that are on the smaller side—they’re more flavorful. You can also use frozen blueberries, if you do, don’t thaw them prior to adding them to the batter, add them frozen.
  • Raw sugar (turbinado): a little sprinkle over the batter creates crunchy sweet muffin top.
A blueberry muffin set on a countertop.

How to Make Whole Wheat Blueberry Muffins

First things first, read over the recipe and make sure you have everything you’ll need. Get out a few mixing bowls, a microplane, whisk, rubber spatula, muffin pan, and cupcake liners.

  1. Preheat your oven to 425ºF before you even get started measuring out ingredients or mixing up the batter. 
  2. In a large bowl whisk together the flour, cornstarch, baking powder, baking soda, and salt. 
  3. In a medium bowl whisk together the yogurt, honey, oil, eggs, lemon zest, and extract until smooth. 
  4. Add the yogurt mixture to the flour mixture and mix until nearly combined but a few pockets of flour remain (this is key, don’t over mix!).

  1. Toss the blueberries with a teaspoon of flour (this helps them from dropping to the bottom of the batter). 
  2. Add the blueberries to the batter and fold in JUST until combined. Again, avoid over-mixing! 
  1. Divide the batter between lined muffin cups (about 5 tablespoons per cup). 
  2. Combine turbinado sugar with lemon zest and sprinkle evenly over the cups of batter.
  3. Transfer the muffin tin to the oven and bake muffins at 425ºF for 5 minutes. Keeping the muffins in the oven, decrease the oven temperature to 350ºF and continue to bake until a toothpick inserted in the centers comes out clean, about 18 minutes more. 

You can also watch the Web Story on how to make these Healthy Blueberry Muffins!

Expert Tips

  • To get that bakery-style domed muffin top, the trick is to start baking at a high temperature in the oven (this activates the leavener). After a few minutes, drop the temp down to a medium heat (350ºF or 375ºF) to encourage even baking. This ensures the outside and inside of the muffin cook at the same rate.
  • Don’t be afraid to fill your muffin cups to the top! The same can’t be said for cupcakes as they often have a thinner batter. But with a thick batter like this one, it’s important to fill the cups full. 
  • Undermix the batter, sounds crazy, but it’s good to have lumps in your muffin batter. This ensures the muffins and light and tender when baking.
  • Toss the blueberries in flour to prevent from sinking. By doing this right before you stir them into the batter, it keeps them floating within the muffin rather than collecting at the bottom.
  • If it’s not blueberry season, frozen blueberries also work well. Wild berries are even better for their natural sweetness!
A blueberry muffin set on a countertop with a bite taken out of it.

Substitutions for Healthy Blueberry Lemon Muffins

These healthy blueberry muffins have a couple ingredient swaps that make them healthy without sacrificing taste. I’m sharing some of my best tips when it comes to lightening up baked goods. Plus, I wanted to make sure I shared some other ingredient substitution recommendations too.

  • The first trick to creating healthy muffins that don’t taste healthy is to use whole-wheat pastry flour—one of my all-time favorite ingredients to bake with. Whole-wheat pastry flour is a great way to create 100% whole-wheat baked goods that aren’t too dense (regular whole-wheat flour can be heavy and dense). Plus, I love that it adds a nutty, toasty flavor to muffins, cookies and breads. 
  • Another great hack is to add a bit of cornstarch whenever you’re baking with whole-wheat flour. Cornstarch is a key ingredient in cake flour and/or cake recipes because it helps to create a tender crumb (which is important when baking with denser whole-wheat four). 
  • My third trick—use natural sweeteners. Natural sweeteners like honey, maple syrup, agave syrup, coconut sugar, and sucanat add more flavor than regular refined sugars and are much better for your blood sugar levels.
  • Add protein and moisture with yogurt. We use Greek yogurt in this recipe, it adds a great tangy flavor that brings out the natural sweetness of the honey and berries. It also adds protein to the muffin, which is great for a healthy recipe.
Healthy blueberry muffins in a muffin tin.

Storage instructions and freezing

  • On the Counter: Stored at room temperature, lemon blueberry muffins will keep for two days. 
  • For the Fridge: Stored in an airtight container in the refrigerator, these muffins will last for up to 1 week. 
  • For the Freezer: Place in a ziptop bag or freezer-safe container and freeze for 1 to 2 months. Thaw on the counter overnight.
  • To Reheat: I prefer the quick microwave-method for reheating muffins. They don’t need much time, 10–15 seconds is all. You can also reheat these in a 300ºF oven until warmed through, 5–8 minutes. 
A blueberry muffin set on a countertop with a bite taken out of it and honey dripping down it.


How do I prevent whole wheat desserts from being too dense?

Use whole wheat pastry flour rather than regular whole wheat flour. It’s finer and lighter in texture which prevents the muffins from being chewy.

How do you keep berries from sinking in muffins and cakes?

Toss them in a tablespoon or so of flour before stirring them into the batter. This keeps the berries suspended in the muffin.

More Easy Muffin Recipes Like This

Whole Wheat Blueberry Muffins

4.62 from 39 votes
Prep Time 15 minutes
Cook Time 25 minutes
Total Time 40 minutes
Yield 12 muffins
Category Breakfast
Cuisine American
Author Lauren Grant


Light, tender and bursting with blueberry flavor, these perfect Whole Wheat Blueberry Muffins are 100% whole-wheat, naturally sweetened, and made with heart-healthy olive oil!


  • 2 ¼ cups (245g) whole-wheat pastry flour + 1 teaspoon for blueberries
  • ¼ cup (35g) cornstarch
  • 1 ½ teaspoons (6g) baking powder
  • ½ teaspoon (2g) baking soda
  • ½ teaspoon (4g) table salt
  • 1 cup (227g) plain Greek yogurt
  • ½ cup (172g) honey
  • cup (67g) olive oil
  • 2 large eggs (100g)
  • 2 lemons, zested
  • 1 teaspoon pure almond extract or vanilla extract (5g)
  • 1 ½ cups (214g) fresh blueberries
  • 2 tablespoons turbinado sugar, optional


  • Heat oven to 425°F (218°C). Line a 12-cup muffin tin with cupcake liners (or grease the cups with nonstick spray).
  • Whisk together 2 ¼ cups flour, cornstarch, baking powder, baking soda, and salt in a large bowl, set aside.
  • Whisk together yogurt, honey, oil, eggs, 1 tablespoon lemon zest, and almond extract until smooth.
  • Add yogurt mixture to flour mixture and stir until mostly incorporated but some pockets of flour remain.
  • Toss blueberries with remaining 1 teaspoon flour to coat; fold blueberries into the batter just until combined.
  • Divide batter (it will be thick) between muffin cups, about 5 tablespoons per cup. Combine turbinado sugar with 1 teaspoon lemon zest and sprinkle evenly over cups of batter.
  • Bake muffins 5 minutes at 425°F then, keeping muffins in oven, reduce oven temperature to 350°F (177°C) and bake until a toothpick inserted in the centers comes out clean, 16–18 minutes more. Total bake time is about 23 minutes.
  • Transfer muffin tin to a wire rack and cool 5 minutes, then transfer muffins from pan to wire rack to cool completely.



GREEK YOGURT: I use nonfat Greek yogurt, but you can use 2% or full-fat as well. Just make sure to use Greek yogurt. You can also substitute sour cream for the Greek yogurt here.
BLUEBERRIES: fresh blueberries are best here (I like to seek out blueberries on the smaller side—they’re more flavorful). You can also use frozen blueberries, if you do, don’t thaw them prior to adding them to the batter, add them frozen. Lastly, if you’re using frozen, try to find some frozen wild blueberries, they add tons of flavor!
TURBINADO SUGAR: turbinado sugar is raw sugar (i.e. Sugar in The Raw) and has a coarse texture. Not only does it add a dose of sweetness, but it also adds some crunch. You can skip using it, or you can use regular sugar, sucanat or coconut sugar instead.


Serving: 1muffinCalories: 150kcalCarbohydrates: 21gProtein: 4gFat: 6.5gSaturated Fat: 1gCholesterol: 31mgSodium: 116mgFiber: 2gSugar: 15g
Like this? Leave a comment below!I love hearing from you and I want to hear how it went with this recipe! Leave a comment and rating below, then share on social media @zestfulkitchen and #zestfulkitchen!
A blueberry muffin set on a countertop with a bite taken out of it and honey dripping down it.

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About The Author

Lauren Grant is a professional culinary food scientist, food writer, recipe developer, and food photographer. Lauren is a previous magazine editor and test kitchen developer and has had work published in major national publications including Diabetic Living Magazine, Midwest Living Magazine, Cuisine at Home Magazine,,, and more.

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How many stars would you give this recipe?


  1. 5 stars
    These muffins have the best texture and great flavor to back them up! I love that they aren’t too sweet! The turbinado lemon zest topping adds the perfect crunch! Thank you for this delicious, healthy muffin recipe!!

  2. 5 stars
    I love that tip to bake them at a higher temperature first and then drop it down – perfect muffins every time – thank you for the delicious recipe, obsessed!

  3. 5 stars
    Blueberry and Lemon is one of my favorite flavor combos! I made these and am embarrassed to say we ate them in 2 days! Will definitely make again when we pick fresh berries this summer.

  4. 5 stars
    I made this recipe last night and my wife and mother in law loved them, so gave it 5 stars. I feel they are a bit dry, which I attribute to something I can do better, so what would you suggest to make them just a bit more moist?

    1. Hi Chuck, thanks for the comment and for letting me know you found them to be a bit dry. The first thing that comes to mind is to make sure you are fluffing the flour a bit before you measure it out. This is important for all types of flour, but especially whole-wheat because it can become pretty compact over time as it sits in the bag. The second thing I recommend trying would be to decrease the bake time by a couple of minutes or so. I would try reducing the last segment of baking (after you’ve reduced the oven temp) to 14 minutes or so—but I would be sure to check with a toothpick to make sure the centers aren’t too under-baked. Finally, I would be really careful not to over mix—a few pockets of dry flour is OK!

      I hope that helps, let me know if there is anything else I can help you with!

  5. 5 stars
    Quality recipe – great instructions and tips. Mine rose even higher than yours, and were moist and fluffy!

    I second that they were less sweet than most muffins, but I like this because it makes me feel like less of a pig when I inevitably eat 3 muffins fresh out of the oven.

    I used light sour cream (that’s all we had) and didn’t do the topping, but wished I had done it because there wasn’t much lemon flavor. Still yummy though!

    I’ll be using your tips in future muffin recipes and trying out your other recipes. Thanks!

    1. Hi Mimi! I’m so glad you enjoyed these muffins—you’re right, the topping adds a ton of flavor. If you want to skip the topping next time, I would add more zest to the muffin batter to enhance the lemon a bit more.
      I’m glad the light sour cream worked well, and I love that they rose higher than mine. It always makes me happy to see a tall-domed muffin! 🙂

    1. Hi Chelsea! The muffins might come out slightly more dense, but white whole wheat flour should work just fine! Let me know how it goes!

    1. Hi Bethany! Great question, I haven’t tested this recipe with coconut oil and the two oils are quite different, but I think it should work just fine if you use melted coconut oil. You can also use vegetable oil instead of olive oil. Let me know how it goes!

    1. Hi Leah,

      I haven’t tested this recipe using kefir, so I can’t be positive if it will work well. Kefir is so much thinner in consistency than Greek yogurt, I worry it will make the batter too loose. If you do use Kefir, I would use 3/4 cup kefir (instead of 1 cup yogurt) and 1/4 cup olive oil (instead of 1/3 cup). Let me know how it goes!

    1. Hi Monique, I have not tested these muffins with plain flour and can’t guarantee how they’ll turn out. But I do think it should work OK! I would start by decreasing the total amount of flour by 3 tablespoons. If the batter looks thinner than the step shots in the article above, go ahead and add a tablespoon when folding in the blueberries. Let me know how it goes!

  6. Why is cornstarch important in the recipe… my daughter is fructose intolerant.. is there a cornstarch substitute or use 1/4 cup less flour and delete adding cornstarch?less

    1. Hi Julia,

      Cornstarch helps to create tender muffins. This is important for muffins in general, but especially with whole-wheat muffins. You can try using arrowroot starch instead, or leaving it out altogether and adding an extra heaping tablespoon of flour to the batter. I haven’t tested either of these changes, but the muffins should still turn out well! If you skip adding the arrowroot starch, the muffins will be slightly more dense. I hope that helps!

  7. 5 stars
    I love this recipe. I accidentally left out the olive oil but they still came out fine, thankfully. Lemon and blueberry are one of my favorite combinations and these taste so so good. 12/10 would recommend to someone.

    1. Hi Izzie! I’m so glad they still turned out well without the oil! Thanks so much for trying them and leaving a review, I love this recipe and am glad you do too! 🙂

  8. I made these into mini muffins and cooked for about 13 minutes….I was surprised they never changed shape and came out VERY dry I’m afraid. Not a hit with my family unless coated in butter and eaten with tea / coffee. Sorry…won’t be making again.

    1. I’m sorry to hear they did not rise, that shouldn’t be the case with this recipe using both baking soda and baking powder. I would double check the expiration date of the baking soda and baking powder to ensure they are activating as needed.

  9. 5 stars
    Just made this recipe. I tweaked a little bit. Used coconut oil instead of olive oil. Also, used a little bit less oil, maybe a tablespoon less, and replaced it with unsweetened apple sauce. Also added an extra 1/2 cup of berries. Didn’t have turbinado sugar so i just used 1/2 tablespoon of white sugar with the lemon zest. These are some of the best muffins I’ve had in forever. You can totally taste the difference between these (wholesome, not overly sweet, healthy tasting) and store bought (way to sweet for me and wayyy more calories)! Thanks for this recipe, it is a for sure KEEPER!!!

  10. 5 stars
    The best blueberry lemon muffin I have ever made and I have tried a lot of healthy muffin recipes. I did add lemon juice from half of the lemon and it all balanced out from the extra flour that I bathed blueberries in. Thank you, thank you, thank you!

  11. 1 star
    I typically believe if you have nothing nice to say, don’t say anything. However, these were such a waste of time, effort and quality ingreds, that I have to post.

    They were way too dry. I followed the recipe exactly. I think it’s just not a good recipe. It needs less flour or more moisture. Mine came out super dry and not good flavor wise. I make lots of healthy recipes, too, so I know what it should’ve been like.

    This recipe would be better with less flour (and/or a mix of whole wheat and white flour) and the addition of unsweet apple sauce. I wouldn’t even try to fix it though. I would just choose another recipe.

    I also want to point out that I made these virtually with a friend in Colorado. We’ve been doing virtual bakes at least 2x a month for the past year. We do this often and have tried tons of recipes. We are advanced bakers at this point. Her muffins were better than mine. She weighed her flour and added the juice from the lemon. While hers are edible, she didn’t think they were “good”!

    1. Hi CG, I’m sorry to hear they did not turn out well for you. I have never experienced these coming out too dry and without further information it’s hard to pinpoint the issue. A few things are important to these muffins coming out tender and “moist.” It’s imperative to only let them rest in the tin after baking for 5 minutes and to use whole-wheat pastry flour (not regular whole-wheat flour). As you mentioned being an advanced baker you probably already know the importance of having an over thermometer to verify the temperature of your oven in addition to not baking on convection. It’s also important to make sure the baking powder and soda being used are not expired. Lastly, weighing the ingredients does help to create the best possible muffin. If you don’t have a scale, it’s important to measure the flour by first fluffing it with a spoon, then spooning it into the measuring cup and leveling.
      As for not being “good,” I do want to reiterate that these are not meant to be overly sweet which is one reason some people might not like them as much as highly sweetened muffins.

  12. 5 stars
    Hi! I’m back to this Grant-astic recipe for like the fourth time, and wanted to add that I’ve tried making these with white flour when that was all I had, and they still turned out well (although a bit less healthy)!

    Just a note, I noticed that the instructions say “transfer to wire rack to COOK completely” rather than COOL. I briefly wondered whether I’d been making them wrong all along, haha.

    By the way, for the potential Negative Nancies out there: If a recipe that others love didn’t turn out when you made it, something probably went wrong in your process. It doesn’t prove that the recipe is bad and deserves to be slammed! Either try to figure it out or just move on.

    1. Hi Mimi! Thank you so much for the comment! And my goodness—what a typo on my part! That’s been updated, thank you for letting me know! And for the kind comment! 🙂

  13. 5 stars
    These are amazing! I didn’t have whole wheat pastry flour so I did a mix of whole wheat and all-purpose.

    1. Hi Sherry! I’m so happy to hear you like them! Glad the mix worked well, that’s a helpful note for other readers.

  14. 5 stars
    Amazing! These are my new favorite muffins. I added lemon juice to add more lemon flavor and they turned out fluffy and flavorful. I will be making again.

  15. I want to make mini muffins with this recipe. Can you tell me the correct baking time?


    1. Hi Michele!

      Great question, I haven’t tested this but I would bake them at 350°F for 12-14 minutes. If you have them, paper liners are great. If not, make sure you grease the muffin tin. You should get 36-40 mini muffins. Let me know if you have any questions, and I’d love to hear how they turn out!

  16. Just an FYI, the calorie count listed is off by quite a bit. I followed recipe exactly, minus the topping, and calculated 222 per muffin.

    1. Hi Chelsea, great question. I haven’t tested this—but I think you should be able to freeze them with success. Once the muffins are baked and cooled completely, I would wrap them in plastic wrap, then in foil then place them in a resealable zipper-lock bag. To thaw, I recommend unwrapping them and thawing at room temperature. Let me know how it goes!

  17. These muffins are so delicious! I swapped out the cornstarch and replaced it with dry milk powder because I like the flavor. Thank you so much for sharing this amazing recipe!!

  18. Made these this morning. Very tasty. I’d like to make them into. Protein muffing. What would you recommend to accomplish that?
    Thanks, Laura

  19. Hello! I am trying to make this recipe using nothing but a digital scale since I can get more exact measurements and that’s all I have at my disposal; how can I convert everything into grams? Please advise!

      1. Thanks so much Lauren. I made these and loved them so much, they were the most perfect muffins. If I wanted to change up the flavor and make them pumpkin chocolate chip, how could I do so?

  20. 5 stars
    I made as directed, except I also added 1/2 teaspoon lemon extract. These were perfectly fluffy, tender, moist, and delicious. My ultra-picky kids gobbled them up, which is a small miracle in itself. Thanks for another amazing recipe!

    1. Woo! So glad you and your kids enjoyed these! Great idea to add lemon extract for an added boost of flavor!

  21. Substituted King Arthur GF 1:1 flour and sour cream for yogurt/brown sugar on top because I had them already in my kitchen. Delicious! Will make this recipe again.

  22. 5 stars
    They are still in the oven cooking! 6 minutes to go. My husband walked in the house and said how great it smells.
    Can’t wait to try one!

  23. 5 stars
    Hello everyone! These lemon blueberry muffins came out absolutely amazing with fabulous texture. I have literally eaten two already. I will admit. They are not sweet due to the blueberries. Then again, I don’t think blueberries are in season right now. But hey, that’s all right. There isn’t anything a little honey can’t fix. I did not follow the grams in the recipe. The following adjustments were made. I used 120 g equivalency to 1 cup of pastry flour. So 270 g (2 1/4) of whole wheat pastry flour and 30 g of cornstarch which would be equivalent to a 1/4 cup. I sifted my dry ingredients and incorporated the Himalayan pink salt after(pink salt will not sift through). I used granulated sugar. I forgot to get the turbinado yesterday, when I picked up the whole wheat pastry flour at Whole Foods. This was really a very easy recipe. Just make sure you have all of the ingredients and your muffins should turn out amazingly without any issues. I will definitely try this recipe again when blueberries are in season for me. Thanks so much for the fantastic recipe!

    1. Hi Laura, thanks for sharing your insights and what you did with this recipe. So helpful for other readers. I’m so glad you enjoyed this recipe and thanks for leaving a review!