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
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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.
I made these muffins last week, using vanilla greek yogurt that I had on hand, and they were so delicious, probably the best muffins I’ve ever made. I look forward to sharing them with my family and friends. Making another batch later today!
Made these muffins this morning before our Arizona temperatures got too warm to heat up the kitchen. So delicious and nutritious. Easy recipe and baked up beautifully. Definitely a brunch item or late night snack.
Excellent recipe! I used the King Arthur gluten-free flour blend and So Delicious coconut yogurt. The muffins turned out great! Will definitely make this again.
I made these blueberry muffins yesterday, used flax eggs, and they turned out moist , delicious, and definitely not enough☺️
Thanks for the great recipe
I love this recipe!! I want to make these again but I only have spelt flour. I’ve heard it can be a 1:1 substitute with wholewheat flour…would it work in this recipe? And if so, would you recommend any other modifications?
Thanks Kate :)
Hi Michaela! I haven’t tried spelt flour with this recipes, so I’m not quite sure. However, I do know it works in my banana bread recipe so it would be worth trying. Let me know if you try it and the result!
Awesome Recipe! Can I check whether it’s ok to substitute wholewheat flour for spelt flour? Any modifications required to make this work?
(sorry if this is repeat posting, my previous message didn’t seem to post!)
Thank you :)
Hi Michaela! I haven’t tried spelt flour with this recipe. I do know it works in my banana bread, but not sure in this application.
Made this recipe yesterday for a friend with diabetes. Only had dried blueberries so soaked in hot water to soften. He said they were wonderful! He generally doesn’t comment on my baking except to scarf them down so this is a real endorsement
I’m happy to hear that, Angella!
Have lots of blueberries on hand and wanted to make these, but flour is still hard to come by these days. I do have extra coconut flour on hand. Do you think it would work here? At the same amount or should I adjust the flour? Thanks!
Hi Cecilia! I’m sorry, coconut flour is not a good substitute. I don’t find it works well as it soaks up all the moisture.
Hello! I don’t have any yogurt on hand but want to make these tonight :) can i sub with something else, like almond milk? ps love your recipes!
Hi Caroline! What did you end up doing? I would suggest following my vegan alternative in the notes if you can. Let me know how it turns out for you!
Loved this recipe! I used gluten free flour. I didn’t have raw sugar, I’ll try that next time. My granddaughter has many food allergies and these would be prefect for her.
Muffin are good but mine tasted dry. What did I do wrong?
Hi! I’m sorry to hear that. I wonder if you may have left them in the oven a little too long. How long did you bake them for?
YUMMM!! These make making better choices with food easy!! My toddler and husband absolutely loved also! Thank you for this fantastic recipe!
I did do 1c whole wheat flour and the 3/4c white flour because I’m easing back into the healthy eating game. I’m going to use all whole wheat flour next time! Thanks again!!!
These are delicious! Since this era has resulted in a shortage of flour at my local stores, I was only able to get my hands on bread flour. And oh my goodness!! They are so good this way! I am looking forward to trying more of your recipes!
Could I add grated carrots? How would that change the recipe or cooking?
Thanks!
Hi Rachel! Unfortunately, that would change the entire recipe as carrots provide their own amount of moisture. Not sure if you have tried my carrot muffin recipe yet.
I don’t have quite enough honey or maple syrup to get a full half cup. Do you think it would be OK to use both honey and maple syrup to get to 1/2 cup? Like 1/4 cup of each?
Hi Jen! That should work. Let me know if you try it!
Hi Kate,
Can I swap out the wheat flour with almond flour ? Will it effect the texture and quality of the muffins?
Hi Saira! Unfortunately, almond flour doesn’t work well in my experience as a 1:1 substitute.
Delicious! My new best recipe for Blueberry muffins. Just printed your Raspberry Lemons Muffins. Making they next!!
Have made these so many times with all purpose and they have been perfect.
Today, I tried them with white whole wheat flour as the recipe originally calls for and Felt they were drier and lacked sweetness .
Is whole wheat flour drier then all purpose flour ? I’m trying to figure out what went wrong
Hi Saira! I’m sorry to hear that. How did you measure the flour? You may have added too much or maybe baked too long.
Hi! I wanted to make these today and have gotten everything ready! I was just wondering; when using spelt flour instead, should I use the same amount of flour? Also, say I wanted to use barley flour, would that be okay? If so, should I use the same amount of barley? Or perhaps a blend of spelt and barley? What measurements would I use then? Sorry for all the questions, I hope you can answer at least some of them!
Thank you x The recipe looks amazing!
Hi Fatimah! I haven’t tried spelt flour in this recipe. I do know it works in my banana bread recipe as a 1:1 replacement, so may be worth testing out. Be sure to report back! For the barley question, I’m not sure. Sorry!
Tried it.love it.mom loves it, mother-in-law loves it Thanks for the awesome recipe kate!
Are these freezable, and if so what’s the best way to defrost them
Doubled the recipe and made vegan with old coconut yogurt that had turned just a bit sour. Really enjoyed this, maybe the best muffins I’ve had. Thanks so much! A breeze to make, too!
I made these muffins 2 months ago and they turned out perfectly! Can I also mention that this is the first time that i have ever baked ANYTHING at all – I’ve never made muffins, baked a cake, bread or cookies and even for me this recipe and the steps were easy to follow and everything was explained really well. Thank you Kate, baking is much less daunting for me now.
Hello! I’ve made your banana and zucchini bread recipes and love them!
Question on this recipe, I’d like to add some oats, how would I adjust the flour?
Hi! After a bunch of recipe testing, I’m pleased to report that you can add up to 1/3 cup old fashioned oats to any of my muffin recipes.
Hello again!!
The muffins came out flat but tasted great, even more so the next day! I don’t know if the way they didn’t rise was because of the flour, the silly mistake of not using a muffin tin, or whisking the wet ingredients far too much with my electric whisker thingy. Oh well.
I do know about your banana bread! That was the first thing I’d ever baked, and my family loved it to bits. I hold that recipe dear to my heart, hahaha.
Thanks for the reply!
Hi Kate,
Thanks for the Recipe.
I will try it this evening.
I do not have any greek yogurt or any yogurt.
Sooo, I looked on the Internet for a substitute!
And low and behold one of the choices I actually have!
Mayonnaise!
I will try it!
It is a good quality Olive Oil based mayonaise.
Sincerely,
Matthew
Great recipe! My kiddos love it, on top I always add a crumble of honey, oats and butter, delicious ..Thank you!
These turned out AMAZING! Approved by my children as well and the neighbor kids whose mom asked for the recipe after her kids begging for more! I used honey and I only had vanilla Greek yogurt on hand. Used whole wheat flour for it. A little extra cinnamon than called for (I love cinnamon) and more blueberries than called for because I had so many! They are soooo good! Thank you for the recipe! I highly recommend. They come out so moist! Oh and I should add I made them mini muffins because they are easier for my kids to eat.
I’m glad they were such a hit, Kristy!
First off, I love your blog and have been so pleased with your recipes. Always looking for lower sugar naturally sweetened things that still taste great, so thank you! I was looking for a naturally sweetened blueberry muffin recipe but really wanted some lime kick to it, so followed your recipe as is but zested two limes in place of the cinnamon and it was seriously awesome. I rarely leave reviews but felt compelled to this time! Thank you!
I like your take on this one, Michelle! I love your creativity.
Hi, I don’t have Greek yogurt can I use normal vanilla yogurt?
Thanks
Hi Chui! I would suggest using the vegan alternative recommendation.
I made this with nonfat, plain Greek yogurt, white whole-wheat flour, and chocolate chips (no blueberries). They were very disappointing and dry. Very dry. I think the blueberries add moisture and taste better. Maybe you have another recipe for chocolate chip muffins or I need to use whole fat yogurt. Either way, the nonfat yogurt did not provide enough moisture. I have made this recipe with blueberries and whole fat yogurt and it’s delicious and moist.
Hi Judy, I’m sorry to hear you didn’t love what you tried. Yes, these are specific to blueberries as to your disappointing results. I know several readers love my banana muffins with chocolate chips. Maybe try that?
I am so glad that I found your blueberry muffin recipe . My son was diagnosed with Crohn’s last week and we had to make dietary changes. Every ingredient you use in this recipe is on his approved list of foods .( I just left out the sugar to sprinkle on top ) I used regular yogurt And honey which made the muffin moist and creamy .
You made my 11 year old very happy and not deprived of having a baked good . Can’t wait to try more muffin recipes ! Thank you again .
Melissa
I’m sorry about your diagnosis! Thank you for sharing that this one works for you and that your kiddo likes it.
Came across CookieandKate in March and have been endless recipes, all of them I love. Favorites are this one and the banana bread. Having a baked treat to look forward to in the morning with coffee is such a good way to start the day and your clean, healthier recipes are the best!!! I added strawberries this time and I’m anxious to see how the turn out. I also though I’d make 10 larger cupcakes instead of 12 but looking into the over, seems like a mistake haha. Thanks for these recipes! Great tips and organization.
My whole family loved these! No one was able to tell that they were healthy, and these are just as good as, if not better than, the sugar-filled batters from the store. Definitely a go-to recipe!
I’m excited they were a hit! Thank you for taking the time to share, Kal.
Just made this. So delicious! I replaced a cup of the wheat flour with ground oats. Turned out so moist and just the right amount of sweetness. Thank you for sharing!
I made these for my co-worker’s birthday, and they came out great! I’ve actually never met a blueberry muffin that I liked; I find the ones typically sold in bakeries and coffee shops to be sickeningly sweet, but I loved these! I used maple syrup and frozen blueberries in my batch. My co-worker approved, and so did my family (we took a lil baker’s tax… as one should) They stuck to the paper liner a tiny bit, but not so much to where you lose a significant percentage of the muffin. Thanks for the recipe, Kate!
I’m happy you approve of them! Thank you for sharing, Oksana.
Thanks for the great recipe! They cooked up beautifully and were delicious!
Hi Kate,
I made your blueberry muffin recipe for the first time.
They were delicious and moist.
I did not make any changes and used whole wheat flour. Moist with delicious blueberries and great for breakfast and freezing.
My husband wants me to add more sugar because he’s use to the sweet muffins at the grocery store. I will tell him to add a little maple syrup instead/I won’t change the recipe.
Thank you for such great recipes….Doreen
LOVED this recipe! However, I put them in an air tight container & they started to mold after 3 days, any ideas why or a better way to store them?
Hi Kat, 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. Looks like you had them out a little too long. I hope you were able to enjoy some before they went bad!
I apologize! Guess I can’t read. I see the eggs listed! In your Healthy Blueberry muffin recipe. Omg so sorry.
No problem, Jean! I’m glad you guessed two eggs. Hope you love the muffins. :)
Tried this recipe using, rhubarb, banana then raspberry and apple chunks as well…perfection!! (Raspberry + apple was my fave). Such a great recipe- I eat at least 1 muffin a day during lockdown haha
Absolutely love these muffins! I’ve never been a successful baker, even with following recipes, it’s always a fail. I saw how simple this recipe is and thought I’d give it a go this morning and they are sooo moist and fluffy! I couldn’t let them cool down, I had to eat a couple immediately! I used frozen blueberries and they turned out fine. I’ll have to add more blueberries next time :)
They were absolutely delicious! My family loved them(I made them a few hours ago and half of them are already gone), thank you!
These have become our go to muffin recipe! They turn out perfect every time. No changes needed, but I usually add chia seeds and mix up the fruit just for some variety. Thanks Kate!
These muffins were AMAZING! My very picky boys loved them and didn’t even miss the sugar. Thank you!!!
Kate- Love this recipe and many others but at 71 living alone I purposefully own a 6 Muffin tin or make 1/2 recipes, for many reasons. :) it would be great if your provided a 1/2 Scale option for at least the FLOUR part or parts of recipes that arent already in TBLS or TSPS. I’m very good at math but it takes a lot for many older folks to divide 1 ¾ cups. Alexa says its 28 TBLS so 1/2 is 14 TBLS which is 3/4 Cup + 2TBLS.
Made these gluten free with Bob’s Red Mill flour and they are DELICIOUS. Thank you for the recipe!!! Will be making these over and over again!
I didn’t have Greek yogurt, and used light sour cream. I also used Tree Hive Maple Honey syrup (it’s just honey mixed with maple syrup) and freshly ground, organic, soft, white wheat, (instead of hard white wheat) and these are delicious! So light, moist, and the perfect amount of sweetness. Thank you!
Where can you get white whole wheat flour I’ve looked everywhere. The only place I’ve found it has been Amazon and its outrageous $$$$
Hi Tara! It’s been tricky to find recently. You can try whole wheat flour instead. Whole Foods has had it and Trader Joes.
Very tasty and healthy!
Hi, I just made these and they came out great! I used one cup of whole wheat flower and the rest white and I thought it was perfect. Thanks for the recipe.