Healthy Blueberry Muffins
These healthy blueberry muffins are golden, fluffy, moist and delicious! No one will guess this recipe is made with 100% whole wheat flour and naturally sweetened with honey or maple syrup.
Updated by Kathryne Taylor on August 30, 2024
When you buy through our links, we may earn a commission. Learn more
Would you look at those blueberry-studded beauties? These blueberry muffins are golden on top, and moist and fluffy on the inside.
Best of all, they’re bursting with jammy blueberry flavor. These are my favorite homemade blueberry muffins, and it’s about time you met them.
These healthy blueberry muffins are easy to make, too. Forget those box mixes! You can make these wholesome muffins from scratch with basic grocery store ingredients. No special equipment required.
What makes these blueberry muffins healthy?
These muffins are more healthy than your average blueberry muffins. They’re made with 100 percent whole wheat flour (I used white whole wheat flour, which you can hardly taste). Whole wheat flour offers redeeming whole grain nutrients and extra fiber.
The muffins are also naturally sweetened with honey or maple syrup, which lend subtle honey or maple flavor to the muffins. They’re lower in overall sugar content compared to coffee shop muffins.
Last but not least, I used Greek yogurt instead of sour cream, which lends the same irresistible tang but with more protein and less fat. I don’t think that yogurt passes for sour cream on tacos, but it totally works in muffin recipes.
Blueberry Muffin Recipe Tips
You can make these muffins with fresh or frozen blueberries. Do not defrost frozen blueberries before using; just stir the frozen blueberries into the batter as directed.
Tossing the blueberries with one teaspoon of flour prevents them from sinking to the bottom. This way, you can use a full cup of blueberries without risking the integrity of the muffins.
Sprinkling 1 tablespoon of raw sugar on top of the muffins before baking yields deliciously sweet, crackly muffin tops. You can buy raw sugar in the sugar aisle of most grocery stores these days, or just grab a few extra raw sugar packets from your go-to coffee shop (I won’t tell).
These muffins taste best after they’ve had time to cool completely. Or better yet, let them rest for a couple of hours at room temperature before serving. This is true for most baked goods!
Recommended Equipment
I love this sturdy, made-in-the-USA muffin pan (affiliate link). I don’t ever have to grease it, thanks to the silicone non-stick coating. Clean-up is a breeze, too. I’ve never had to soak or scrub on this pan.
Watch How to Make Blueberry Muffins
Love these muffins?
Here are more of my favorite naturally sweetened, whole-wheat muffin recipes!
- Healthy Apple Muffins
- Healthy Banana Muffins
- Healthy Carrot Muffins
- Healthy Raspberry Muffins
- Healthy Pumpkin Muffins
- Healthy Zucchini Muffins
Please let me know how these muffins turn out for you in the comments! I’m always so eager for your feedback. Be sure to check out my Blueberry Scones as well.
Healthy Blueberry Muffins
These healthy blueberry muffins are golden, fluffy, moist and delicious! No one will guess this recipe is made with 100% whole wheat flour and naturally sweetened with honey or maple syrup. Recipe yields 12 muffins.
Ingredients
- 1 ¾ cups plus 1 teaspoon white whole wheat flour or regular whole wheat flour
- 1 teaspoon baking powder
- ½ teaspoon baking soda
- ½ teaspoon fine salt
- ¼ teaspoon ground cinnamon (optional)
- ⅓ cup melted coconut oil or extra-virgin olive oil
- ½ cup honey or maple syrup
- 2 eggs, preferably at room temperature
- 1 cup plain Greek yogurt*
- 2 teaspoons vanilla extract
- 1 cup (6 ounces) blueberries, fresh or frozen
- 1 tablespoon turbinado sugar (also called raw sugar), for sprinkling on top
Instructions
- Preheat the oven to 400 degrees Fahrenheit. If necessary, grease all 12 cups on your muffin tin with butter, coconut oil or cooking spray (my pan is non-stick and doesn’t require any grease). Or, use muffin liners if you prefer.
- In a large mixing bowl, combine 1 ¾ cups of the flour with the baking powder, baking soda, salt and cinnamon. Mix them together with a whisk.
- In a medium mixing bowl, combine the oil and honey or maple syrup and beat together with a whisk. Add the eggs and beat well, then add the yogurt and vanilla. Mix well. (If the coconut oil solidifies in contact with cold ingredients, gently warm the mixture in the microwave in 30 second bursts.)
- Pour the wet ingredients into the dry and mix with a big spoon, just until combined (a few lumps are ok). In a small bowl, toss the blueberries with the remaining 1 teaspoon flour (this helps prevent the blueberries from sinking to the bottom). Gently fold the blueberries into the batter. The mixture will be thick, but don’t worry.
- Divide the batter evenly between the 12 muffin cups (I used an ice cream scoop with a wire level, which worked perfectly). Sprinkle the tops of the muffins with turbinado sugar. Bake the muffins for 16 to 19 minutes, or until the muffins are golden on top and a toothpick inserted into a muffin comes out clean.
- Place the muffin tin on a cooling rack to cool. You might need to run a butter knife along the outer edge of the muffins to loosen them from the pan. If you have leftover muffins, store them, covered, at room temperature for 2 days, or in the refrigerator for up to 5 days. Freeze leftover muffins for up to 3 months.
Notes
Nutrition
The information shown is an estimate provided by an online nutrition calculator. It should not be considered a substitute for a professional nutritionist’s advice. See our full nutrition disclosure here.
This looks amazing! I am unable to find white whole wheat flour. What can I substitute with? Oat flour? Almond flour? I am not on a gluten free diet by the way. Thanks!
These blueberry muffins are fantastic. Our kids absolutely love them. We double the quantity of blueberries since we grow our own and have so many. My question is how well do the muffins themselves freeze for later?
Great to hear, DJ! I find they freeze well for up to 3 months.
Made this recipe. Absolutely love it. It is yummy and healthy. Also, my kids loved it so will definitely become one of our favourites…
Great! Thank you, Melanie.
Delicious muffins! Kids enjoyed helping me make them and then subsequently gobbled them up! I did substitute local Juneberries for the blueberries. Will be making them again soon! Thanks for the recipe!
Thanks for sharing, Maggie! I’m really glad you like them.
My boyfriend and I just made these and they were fun, easy(haven’t baked in awhile..) and super yummy!! Not too sweet( I used raw honey) and very tender yet firm enough to tide you over if ur eating it for breakfast with a banana or a snack :) about to eat another. Thanks!! Give cookie a kiss for me
Thanks for commenting, Julia! If you would like to leave a star review, I would really appreciate it.
Hi,
I like to replace oils in my baked goods with unsweetened natural organic applesauce whenever possible…have you tried the base muffin recipe with this alternative?
Kind regards
I have not with this. I really like the way the oil works with this, especially with the different variations.
for the healthy blueberry muffins can I use almond flour instead of wheat flour?
Thank you!
Unfortunately, that is not a 1:1 substitute. If you are looking to make them gluten free, I would recommend trying Bob’s Red Mill GF flour.
Can I substitute with spelt flour?
Hi unless I’m missing it I don’t see the nutritional value. How many calories in each muffin?
Hi Eileen! The nutrition information is below the notes section. You need to click to expand it. Hope this helps!
Awesome recipe! I have harvested quite a few wild huckleberries this summer, and I was looking for a healthy base recipe to swap in my huckleberries. This is just perfect! I used white AP flour because that’s what I had, with honey.
Thanks you!
Great! Thank you, Ayla for your review.
Overall, these muffins are a great healthy snack! I added more cinnamon, nutmeg, and allspice to give them a little bit more flavor.
Thanks for sharing, Alyssa! I appreciate the review.
These were wonderful! Great texture and flavor! Just a bit of raw sugar on top gave it a perfect crunchy yumminess! Thank you for a great recipe!
You’re welcome!
Hi! I made the muffins yesterday and they’re very tasty overall, but they came out a little dry, so I’m drinking milk to go with the muffins. Do you gave any suggestion on how to make the muffins more moist?
Hmm… I haven’t run into that yet. It could have been that they were baked a little long in your ovens as ovens can vary. Try checking them a little sooner. I always start on the lower end of cooking time and then increase little as necessary. Thanks for your review!
Your recipes are always fantastic and there hasn’t been a single one I haven’t absolutely loved. Your site and cookbook are my go to whenever I bake with the kids because eating healthy is so important to us. I love how your site always has new ideas and I can always find a recipe for a healthy snack quickly. I also love how I can always trust that the recipes will turn out wonderful! Thank you so much for all your great ideas!
I’m so happy to hear that, Teresa! Thanks for your comment.
This recipe is perfection! I made these muffins yesterday and had 1 for a snack today and they are divine. So delicious. Thank you so much for this wonderful recipe! P.S I love ALL your recipes and they are always SO beautiful.
Thank you! I appreciate it. So happy you love them. :)
Hi, would I be able to make these for a gluten-free child without the whole wheat flour and they still taste as good?
The gluten-free options still taste good! Hope this helps.
Holy balls. THESE ARE AMAZING.
I made with flax seed meal as my toddler has an egg allergy. I made with greek yogurt and maple syrup. I will fo sho be making again. Easy and soooooo delicious.
Ha, thank you Amy! I love the excitement.
Delicious!! My whole family loves them!
Great! Thanks for the review.
I came across this recipe because my 6-year-old was home sick from camp on a day they were going to be baking, and he was super disappointed to miss making “sprinkle bread.” He was dubious, but after tasting the muffins, he declared, “There’s no way the camp bread is anywhere NEAR as good as this!” We’d doubled the recipe to last at least a few days, but my 3 sons, their dad, and 2 visiting cousins had devoured all 24 by the next evening! (I had two myself — delicious!)
He has a severe nut allergy and can’t eat the cupcakes his classmates bring in to celebrate birthdays, for risk of cross-contamination at bakeries. When I asked him the other day what special treat he’d like me to leave in his first grade classroom, like oreos or cookies, that he could have when birthday celebrations come up, he paused and smiled at me. “Do you remember those muffins we made when I was sick . . .?” he asked.
Do you think these would freeze ok, to defrost over a few hours in a lunch bag? How long would they last in the freezer?
You know you’ve got a winner of a recipe when even a sugar-obsessed 6-year-old prefers your whole-wheat, honey-sweetened blueberry muffins over Oreos! Thanks so much!!!
I’m sorry to hear about his allergy! That’s hard. But, I’m so glad this is a recipe that works for him and that he loves!! Thanks for your review, Shannon.
I made these muffins today. They are tasty and have a nice texture. I didn’t want to deviate from the recipe as written but I didn’t have enough of the some of the ingredients. I had to use 3/4 cup of AP flour, canola oil, and 1/4 cup of maple syrup plus 1/4 cup of honey. It still turned out well and I plan on making these muffins (and others from this site) again.
Thanks for sharing, Autumn!
Hi what exactly is 1 3/4 cups and 1 teaspoon of flour ? Not very specific is it !
Hi, it actually is a precise measurement. If you read the recipe, you’ll see that 1 3/4 cups of the flour is used in the batter, and then you toss the blueberries in 1 teaspoon so they don’t sink to the bottom.
These look like a great freezer breakfast option for my toddler. Any idea how I would convert the baking time for mini muffins?
I would suggest cutting the time down by at least half and then just adjusting it based on the rate of doneness. I’m not exactly sure timing as I didn’t make these mini-sized. Let me know!
I decided to make half a batch because I wasn’t sure how these would turn out, usually I dont have much success with muffins. OH HOW MUCH I REGRET IT NOW! They are so delicious, light, fluffly and moist that i wish i had more! For my half batch I skipped the honey and instead added 1 tablespoon of brown sugar to the dry ingredients (because i’m baking for diabetics) and added about 2 tablespoons more olive oil to make up for the liquid and they turned out perfect!
You better make a full batch now! :) Thank you for sharing and reviewing the recipe.
I love these blueberry muffins. I’ve tried several recipes for muffins and my husband hated them, but he really liked these. Thank you so much much for sharing! I will be trying other variations.
I’m glad they were a win for you, Allison! Thank you for your review.
My 2yr old and I just made these- they are so good!! Thank you!
You’re welcome, Lisa!
Substituted eggs with 2small bananas, blueberries with golden raisins and honey with jaggery. It was Delicious!!,
Wonderful, Era!
Thank you for the recipe and for making it so versatile! So much of the time when I look up healthy or vegetarian recipes, they are vegan, gluten free, among other things, with hard to stock ingredients, making them unrealistic for our household. I love that you made a basic recipe with options for dairy and gluten, etc. listed after the recipe. It makes it easy for everyone no matter their diet! I will definitely make these. Thanks!
You’re welcome, Holly! I’m glad the substitutions are helpful to you. I would love to hear what you think when you try them!
I have never made From Scratch muffins before. Lots of cupcakes but not muffins. I followed the recipe exactly and step by step. My dough looked like the picture but they batter did not rise. They turned into…biscuits. They don’t taste horrible but they are definitely not fluffy. Any tips?
Hi Brittny, I’m sorry to hear about your muffins! Something definitely went wrong. Any chance you left out the eggs, and/or skipped either the baking soda or baking powder? Those are all essential to making this muffin recipe rise properly.
Awesome recipe. I made it just as the recipe indicated but baked in a bundt pan vs muffin tins. My son loved it for his birthday cake!
I’m glad it still worked in a bundt pan! I appreciate the review.
Made these into mini muffins, baked for 18 minutes..perfect for the littles. Not overwhelmingly sweet but just enough with the sugar sprinkle on top. I used plain yogurt because that’s what I had and you were right- they didn’t rise very much.. not as pretty that way but no one seemed to mind, will be passing this recipe on to friends with kids! Thank you!
You’re welcome, Dani!
Hi Kate! Can’t wait to make this recipe. Does this recipe need to be modified? What would you do for bake time and temp? Thanks!
Hi Phyllis! I want to make sure I understand your question. Modified for what? :)
Hi, I’m from England and am planning to make these muffins (they sound delicious!) but we don’t really measure using cups over here – so to help me get the measurements right please could you tell me how many grams is the equivalent to a cup for both wet and dry ingredients please? thank you :) x
Try this online converter! https://www.myrecipes.com/how-to/metric-conversion-charts
Made these with gluten free flour & applesauce instead of honey & they turn out perfect, there were a big hit. Definitely making them again
Thanks for sharing, Lianne!
How much applesauce did you use? I wanted to try applesauce, but chickened out…
Made the applesauce myself (couldn’t find any in shops near me) Use about 2/3 apples & cooked them in water & then use a blender to get it smooth. Hope it works out for you
Made these tonight. Very easy and look as good as the pictures (can be rare with my cooking ) Smell and taste amazing
Thank you, Jenn!
I have been making your banana bread for months now and we all love it! I have a go-to blueberry muffin recipe, but it calls for WAY too much sugar. I knew there had to be a better way! C + K has not let me down! Thank you! I appreciate your work in doing all the work to develop healthy recipes for us! I can not wait to try them!
You’re sweet, Tiffany! Thanks so much for your review.
They were excellent only they were a bit dry. Next time I’ll add more liquid. I used a GF all purpose flour.
Update: I used Krusteaz Gf all purpose flour and used maybe a tablespoon more yogurt and they were very moist! Perfect! Thanks again!
Sounds very good ,my 10 year old is making some!!
That’s so fun! What did you think, Ryan?
Another fabulous recipe Kate. A friend bought me your cookbook for my birthday. I saw this blueberry muffin recipe in there and made a batch today. So easy and so delicious! My husband and I are going to enjoy these all week long for breakfast. Thank you.
Happy belated birthday! I’m glad you love this and the cookbook, David.
I love your healthy Blueberry muffins. I used coconut yogurt instead of dairy yogurt and instead of honey or maple syrup (which are both to sweet for me) I use Lakanto golden monk fruit or the classic monk fruit. I also use white spelt flour and all my ingredients are always 100% organic which makes a huge difference in taste as well as nutrition.
Thanks for sharing, Terri!
The nutrition information does not show. Could you post it again?
Hi Preeya! You just need to click to expand on the header. If that doesn’t work, make sure you are allowing pop-ups as this is a plug-in to the blog. I hope this helps.
Is there a danger to using more than 1 cup of blueberries? I love muffins that have tons of blueberries…most–both store-bought and homemade–have too few. However, I don’t want the muffins to fall apart either.
Hey Matthew! I love extra blueberries, too. I think you could probably get away with 1 1/2 cups. Please report back if you try!
Thumbs up from my little family! Not too sweet, so you can taste the fruit. They’re lovely warm out of the oven with some cream.
Thank you! I’m glad they were a hit.
Loved the muffins! Thank you – but they got a bit sticky in just a few hours – (left them covered on the counter). Therefore I put in the fridge overnight and warmed in the morning and they were fine. What is the best way to store them>
Can I use muffin paper cups when I bake these? My muffin tray isn’t a non-stick one.
Many thanks!
Rosie
If you need to, that should work fine!
My dough is very thick when making these blueberry muffins. Do you think it is because I used honey instead of maple syrup. Hopefully they will come out okay.
These muffins turned out really well! Everybody loved it! The muffins were moist and not too sweet. We had it warm when it was fresh out the oven (we couldn’t wait) and the blueberries were gooey and perfect. I cannot wait to try more recipes from your website.
That’s great! Thanks so much for your review.
Loved this recipe! I make muffins multiple times a month to freeze for quick breakfasts. These are now added to my list of ones to make. I didn’t have any yogurt, so I used sour cream instead. They still tasted great! Thanks for sharing this yummy recipe!
Thanks for sharing, Lea! I’m glad these have been added to your list.
These look delicious! Could I use regular all purpose flour for these? If so should I use the same amount of flour?
Amazing muffins! I used vanilla greek yogourt, because thats what I had on hand, and they turned out great :) thank you!
You’re welcome! I’m glad you loved them.
So good thank you for sharing!!!! New favorite muffin recipe!!!
Love it! You’re welcome, Katie.
As always, delicious! Only substitution was using a soy based yougourt as that was what I had on hand. Had to cook much longer (34 min). Turned out great!
I’m glad you love it!
Oh..I baked the blueberry muffins today…it was so yumm… I used honey instead of maple syrup, rest everything as mentioned in recipe.I am gonna try carrot muffins too soon. Thanks for super recipe!!
Thank you, Urmila! I’m excited you loved them.
After reading the comments I had to make these! A couple things I did differently – I halved the maple syrup. I used a frozen berry blend which I chopped. And I only had half of a cup of regular greek yogurt so I used a single cup of chobani yogurt, I just scooped off the top and didn’t use the fruit on the bottom. The batter became super sticky and thick once all mixed and I was worried they wouldn’t turn out, but they definitely did :)
I’m glad you had to make them! Thanks for sharing what you did to make them. I’m really happy they turned out for you, Janey!
These were super easy to mix up. They smelled great while baking. They looked picture perfect when taken out of the oven.
Unfortunately they had no taste except for the blueberries and the texture was super funky. I thought I left out an ingredient or didn’t follow the instructions. I re-read the recipe. Check, check and check. Nothing was missed.
It’s a mystery how they were so off vs all the positive reviews. I’ll continue my search for a healthier alternative to the standard blueberry muffin.