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.
Healthy Blueberry Muffins
- Author:
- Prep Time: 13 minutes
- Cook Time: 22 minutes
- Total Time: 35 minutes
- Yield: 12 muffins 1x
- Category: Muffin
- Method: Baked
- Cuisine: American
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 sea 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).
- 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.
Vegetable enthusiast. Dog lover. I'm probably making a big mess in my Kansas City kitchen right now. 
Suzie
I made it. I used coconut flour instead and followed the recipe. Taste delicious.
★★★★★
Freya
It was a total disaster when I used coconut flour
Kate
Hi Freya, I don’t recommend coconut flour. It doesn’t hold up as well and soaks up all the moisture.
Maurice
Turned out very well and tasty…double the recipe I used 3 cups saskatoon berries that grow along the river in Alberta Canada. I used half maple sugar and half honey.
★★★★★
Neil
I just made these and they came out so well, I marched all the ingredients with the addition of adding some chopped walnuts to the batter.
My muffin sections in the pan are large so the recipe made 6 large awesome moist muffins.
Thank you for this amazing recipe my wife lives the muffins although we share one due to size
★★★★★
Liz Coppez
Hi! I love your recipes so much! I’ve made these at least a dozen times. Since my kids are so picky, do you think using homemade blueberry puree instead of whole blueberries would work here? I’d love your thoughts!
★★★★★
Kate
Hi Liz, I don’t know if that would work the same without trying it, sorry!
Beth Sorrell
These are great! I added more blueberries and used sour cream; they were excellent!
Marge Teilhaber
FANTASTIC!!! I used the middle rack for 19M and the toothpick was clean but I gave it 5 more minutes to get more crispness. I just ate 3 of them. It’s SO GOOD! I used frozen blueberries from Costco My tweaks:
1. 1.5C white whole wheat flour + ¼C ground flax
2. No yogurt. Instead did 2/3C unstrained almond milk + 2t apple cider vinegar
3. 7T maple syrup + 1T applesauce
4. 2/3C chopped roasted hazelnuts
5. 1/3C (5T) applesauce instead of 1/3C coconut oil
The 1T of coconut sugar is the perfect amount to sprinkle on each one before baking and it’s a great touch. The muffins are perfect and need no additional sweetness. Next batch I’ll use 1C chopped toasted walnuts and use oat flour with the ground flax and pretty sure I’ll use the same everything. Can’t wait to make this again. Great oat flour primer. I’ll take heed for sure! Kate, great recipe!
★★★★★
Karen
I made these muffins with fat free Greek yogurt, maple syrup and 1.5 cups of fresh blueberries. It made 15 muffins, and they are wonderful!! I chose this recipe for my 1 and 2 year old grandchildren so they could have a healthy snack, but I think this will be my go-to recipe for myself, too, from now on.
★★★★★
Kate
I’m happy they are a hit! Thank you for your review.
Molly
These muffins are delicious! Can I convert this recipe to a loaf pan bread? Thanks!!
★★★★★
Joyce
Agreed do you think that would work Kate? Eager to try soon
Kate
I haven’t tired it, so I can’t say for sure. It will need more time at that same temperature. But again, I’m not sure. Sorry!
Bethanie
This is a wonderful recipe. My husband even loved it and he never eats blueberries, especially cooked. I was shocked when he said he would try one with dinner the other night. Hands down, one of the best healthy muffins we’ve ever had!
★★★★★
Sunny
I don’t have a muffin pan so I made it into a loaf pan (as Blueberry bread), reduced the baking temp to 325F (just like the Healthy Banana Bread) and increased the baking time. I also increased the amount of fresh blueberry to 2 cups. It’s wonderful during blueberry season.
Jo
We don’t often have muffins but my partner said these are the best ones he’s had in a long while and I agree. We added a bit more blueberries and it still worked well.
★★★★★
Kate
I love it! Thank you for taking the time to comment, Jo.
Christine
This is a great recipe. My little boys loved them and so did I! As you bite into them, it smells and tastes like your eating pancakes with apple syrup, just divine! Thank you for sharing and I’ll be trying other recipes on your page
Ada
Awesome! I made these with frozen cherries (cut them in half as directed) and used vanilla greek yogurt and they turned out amazing! Also added 1/4 cup sliced almonds and added a little bit of almond extract in with the vanilla. I love that you offer so many tips on how to modify the recipe. Will try to make a vegan blueberry version next time for my sister in law! Thanks!
★★★★★
Cat
These were delicious, but I wanted to let you know that the cook time in the recipe says 16-19 minutes, but at the top where there’s the yield, author, etc. it still says 22 minutes.
:)
Cat F.
★★★★★
Yvonne
I am not a baker. by any means, and I cannot get over how delicious and perfect these muffins came out!!! Thank you for this excellent healthier version of blueberry muffins!!!
★★★★★
Kate
You’re welcome, Yvonne! I’m glad you enjoyed them.
Melissa
Perfect blueberry muffins! I followed the recipe exactly as written and they were great!
★★★★★
Nicole
Can I use agave syrup instead of honey or maple syrup?
Kate
I recommend what is listed in the recipe, I can’t guarantee the results otherwise.
Paula
Great recipe! I added about a third of a cup of chopped walnuts which worked well.
★★★★★
Claire
These were delicious. A great way to get a healthier alternative for the family. Love that they are not too sweet. Used maple syrup because I’ve always loved blueberries and maple syrup together (think pancakes :)
★★★★★
Kate
I’m happy your family enjoyed them, Claire!
Luann
For being a healthy muffin they taste great! I omitted the fine sea salt and I used a baking soda substitute to reduce the sodium levels to comply with a heart healthy diet. I did not sprinkle muffin tops with sugar but I did use all other ingredients listed in the recipe. When given a choice: I chose to use whole wheat flour, cinnamon, olive oil, honey (raw and unfiltered), and non fat plain greek yogurt. My eggs were not room temp but I did run warm water over the shells prior to cracking them open. They turned out so good. Thanks for the recipe
★★★★★
Diane Whiting
To be honest I almost always steer clear of American recipes. Not just because of the temperatures expressed in Fahrenheit and the weird cup measurements but because I don’t usually like the results which I find fairly tasteless. But I have to say these muffins are very good. I followed the recipe exactly but used proper wholemeal wheat flour- not sure what white whole wheat flour is – sounds like a contradiction in terms. I added a couple of extra blueberries to the top of each muffin just in case I hadn’t got them equally spread out. I used a Greek thyme honey. The texture was very good and the flavour was good, not nasty and overly sweet like shop bought muffins. This let the taste of the blueberries shine through. Well done, great recipe. They are still good and fresh today a day after baking. Thank you. Lovely.
★★★★★
Kate
I’m glad you tried it and enjoyed them, Diane!
Katie Williams
Where’s the dairy free option for this recipe?
Kate
Hi Katie, see the vegan note. That will help!
Mary Ellen Tomaszewski
Delicious muffins. I drink a cup or two of coffee before breakfast and need something in my belly with the coffee. A mini muffin is just right. A regular size is a special treat. So I make a batch, freeze & defrost as needed.
★★★★★
Vera
I’ve made these today and used spelt flour instead and they came out amazing, thank you so much for another wonderful recipe
★★★★★
Kate
You’re welcome, Vera! Thank you for your review.
Mel
I didn’t have Greek yogurt so I just used normal plain yogurt. I didn’t realise it would make it rise less until I put the muffins in the oven, but it came out pretty good but a bit more dense.
It was delicious, the honey made it not so overpowering and overly sweet, which my mum really liked too.
★★★★
Laura
These muffins are INCREDIBLE. Sometimes I like to add some lemon zest and chopped nuts for texture.
★★★★★
Kate
I’m glad that turns out so well for you, Laura! I appreciate your review.
Julia
Hi I would love to make this recipe sounds amazing! Would I be able to substitute the whole wheat flour for almond flour?
Kate
Hi Julia, unfortunately almond flour isn’t a great 1:1 substitute. You could try oat flour if you are needing to make it gluten free. More on oat flour in my How to Make Oat Flour post.
Danielle
Would this work with oat flour instead of WW??? It’s all I have on hand and I really want to make these!
Kate
Hi Danielle, these should work with oat flour. Be sure to follow my How to Make Oat Flour for measurements.
Danielle
Love these!!!! soooo incredibly delicious. I used full fat greek yogurt and oat flour instead of whole wheat because it was all I had on hand at the time and it totally worked! I ended up making 15 because I under filled the muffin tin and they were very small and dainty lol, so if you want a more classic size, fill em up! Highly recommend, can’t wait to make them with whole wheat next time to compare!
★★★★★
Gabriel
Wonderful; thank you for this recipe! I used regular all purpose flour bc we were out of whole wheat–was like a yogurt cake with blueberries. Delicious.
Kate
Overall, great recipe! The muffins aren’t overly sweet, and mine came out moist and fluffy. I would definitely opt for the usual muffin tin instead of minis, as I found the mini muffins didn’t turn out in one piece. I’ll definitely make this recipe again!
★★★★★
Meghan
The recipe says to preheat the oven to 400 degrees fahrenheit but that is too high. Set it to 350 degrees. It came out very dry and chewy due to the high temperature. I would add milk or put less flour to lighten up the thick muffin batter. Overall it was an okay recipe.
★★★
Kate
Hi Meghan, I tested this recipe several times and it works well for me as written. Ovens can vary, so you may be running into that or possibly at a higher elevation than I am in Kansas City. I’m glad you have been able to find something that works for you!
Helaena
Hi Kate, do these freeze well?
★★★★★
Kate
Hi! Most muffins seem to. Let me know how they turn out for you!
Pam Thompson
Love them!
★★★★★
roberta
Great foundational recipe – made 6 large muffins, just adjusted the time. Thanks for the tip to toss the blueberries in the flour!
★★★★★
Jennifer Howay
What could I use as a sweetener with less sugar than the honey or syrup?
Kate
Hi Jennifer, changing the sweetener amount would impact the recipe and I can’t confirm they would turnout.
Kathy
Made this recipe this am and the smell while baking was wonderful. I used the baking time stated at beginning of recipe of 22 mins and they came out a little brown. Wish I’d read to the bottom where your notes were. They are light and have a good texture but I added a scant 1/4 tsp cinnamon and that’s the flavor that comes through loudest. Would leave it out next time.
Valerie
I made these yesterday and they were delicious! I was thinking about trying this recipe with rhubarb instead of blueberries, just to see!
★★★★★
Nat
I milled my own wheat berries for the recipe. The muffins turned out beautifully! Hearty and healthy. Can’t wait to make them again.
★★★★★
Kathy
Made this recipe this am and the smell while baking was wonderful. I used the baking time stated at beginning of recipe of 22 mins and they came out a little brown. Wish I’d read to the bottom where your notes were. They are light and have a good texture but I added a scant 1/4 tsp cinnamon and that’s the flavor that comes through loudest. Would leave it out next time if using blueberries.
★★★★
isaac
Can I use plain flour or does that defeat the whole point?
Kate
Hi, you can but I recommend the flours listed in the recipe.
addison
These are soo good and delicious. Definitely will be making these again. I used oat flour with her oat flour recipe and it tested soo good. The only thing I used different was oat flour. It was a bit chunky but I’m very sure I just didn’t blend the oat flour enough.
BEST EVER!!!!
Denisha
I used coconut yoghurt instead of Greek (I’m allergic to milk). They tasted great however the tops cracked a bit! Any tips on how to reduce cracking?
Kate
Hi Denisha, did they seem dry? If so, maybe reduce the baking time some next time. If they tasted great, I would stick with what you did.
Kim
We absolutely love this recipe and have been making it for years. Do you possibly have a thermomix version?
★★★★★
Kate
Hi Kim, I don’t sorry!
Ariel N
Made these and replaced half of the honey with Natvia (stevia) and used raspberries instead of bluebs. Turned out just as the recipe described and super delicious. Making them again this week, yum!!
★★★★★
Diane
This is a versatile recipe. Made these 3x, they are that good. Want to take it next level? Add the zest from a whole orange.
Also made it for my baby who is egg and dairy sensitive. Substituted with flax egg, and breast milk “buttermilk” and he likes it!
★★★★★
Kate
Thank you for sharing, Diane! I appreciate your review.
MaureenD
Just did these for back to school, and everyone lOVed them!
★★★★★
Kate
Wonderful! Thank you for your review.
Kamala
Planning to make these as mini muffins for my kids lunch. How long should I bake them for 24 mini muffin pan?
Kate
Hi Kamala! It is usually half the time as the original recipe. I would keep an eye on them though. I hope you enjoy them!
Kamala
Thank you! I made them last week into chocolate chip muffins and baked them using timings from another recipe. They came out yummy and used them for my kids lunchbox/snacks.
★★★★
Marie Myers
This is my 3rd time coming back to this recipe -it’s a keeper! I added walnut pieces and swapped 3/4 cup of flour for almond flour and they turned out turned out great
★★★★★
Kate
That’s great to hear, Marie! I appreciate you review.
Joan Horning
These were very, very good. Made them for a diabetic neighbor and ended up eating half of them myself. Used the recipe exactly, had whole wheat pastry flour, and it worked perfectly.
Helen McLean
I made these for my son who has Crohn’s disease. They turned out delicious, as you said a little less sweet but I mistakenly put in 1 1/2 c. blueberries and they were so good. I used whole wheat flour, non fat Greek yogurt and honey and olive oil. Thank you for the recipe!
★★★★★
Melly
ANOTHER 5 STAR RECIPE! I bought your cookbook and almost every recipe I make is a Cookie & Kate recipe. These muffins are honestly the best muffins I’ve ever made; and I’ve tried a lot of muffin recipes. I can’t wait serve them to my kids when they get home from school. Thanks again!
★★★★★
Kate
You’re welcome, Melly! Thank you for your review.
Sue
I have made the blueberry, carrot and apple muffins so far. I like them all. Think the apple is my fav then carrot and blueberry. Fall is here weather is changing pumpkin will be the next one. I have passed the recipes on to others to try
★★★★★
Marieke
I really like your recipes. Tho, when from Europe and thinking in metric sizes it’s super hard to make them. Could you maybe write down the metric measurements as well? A lot of other American websites have this option too
Kate
Hi, I’m sorry to disappoint, but it is not something I offer at this time. Maybe sometime in the future!
Chantelle Lewis
Hello, do you have gram measurements for each of the ingredients? Thank you!
★★★★★
Kate
Hi Chantelle, I’m sorry I don’t provide gram measurements. I know others have found this conversion chart helpful.