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 you 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. 
Ellen Miller
Blueberry muffins are my boyfriend’s favorite, so I’m always happy to try a healthy version. These were delicious! I put in a few extra blueberries (why not?!?) and I’d take the muffins out of the tin and put them on the rack to cool so they don’t over cook. Love these!
★★★★★
Kate
I love that! Thank you for sharing, Ellen.
Anna
This recipe is awesome – have made it twice in 3 days, once with added choc chips and the other time with a crumble topping. The muffins are so soft and perfectly sweet while also being sneakily healthy and got so many comments!! Absolute winner of a recipe, thank you! :)
★★★★★
Kate
I love that! Thank you for sharing, Anna.
Erin Knockwood
Thank you so much for this recipe! Finally a sugar free blueberry muffin recipe that doesn’t have bananas. I’ve made them at least 20 times and they’re perfection just as is! My 4 year old is obsessed.
★★★★★
Francesca Cotrina
Hi! I make them today , I got a perfect texture, they are delicious, but I would like to them to be more sweet . What you suggest me? I used syrup cero sugar , is there any other recommendation?
Thank you
★★★★★
Kate
Hi! You can add some sugar on the top before baking!
Sally
They were lovely thankyou x
★★★★★
Kate
I’m glad you loved them, Sally!
Rebecca Dzhurinskiy
These came out so yummy! Wouldn’t change a thing – they’re perfect! Thank you for the recipe!
★★★★★
Kate
You’re welcome, Rebecca! Thank you for your review.
Sheri Matsumoto
This recipe looks delightful! However, I looked for the buttermilk option you mentioned to make them dairy free and didn’t find it anywhere. I’m allergic to dairy and nervous about putting Greek yogurt in the batter. How much buttermilk do I need to replace the yogurt? Thanks in advance for your answer!
Kate
Hi Sheri! The ratios are in the vegan notes. I hope you can enjoy it!
BRENDA Plummer
HI I used lacto free Greek yogurt from Sainsburys here in the UK and it was perfect.
Kristen
These turned out really well. A little dense, but that could be the wheat flour or the substitutions I had to make due to dietary restrictions. I went with white whole wheat flour, Bob’s redmill egg replacer, refined coconut oil, and so delicious plain unsweetened coconut milk yogurt. I will definitely make them again.
★★★★★
Saaniyah Sajed
These tasted wonderful! Not too sweet, moist, crunchy on top. I baked them on convention at 400f for 19 mins. Wonderful for breakfast!!
★★★★★
Hollie
Hi there,
I would like to make these blueberry muffins however was wondering could I use wholemeal flour instead of wholewheat as there is a slight difference and didn’t know if it would make a difference to the recipe.
Thanks :)
Kate
Unfortunately it would likely impact the outcome of the recipe and need adjustments.
Mary
Hi Kate!
I have sweet super-fatty 10% yogurt on hand. If I omit honey and oil and replace that with more yogurt, is this going to be a complete disaster?
Kate
Hi! Sorry, I wouldn’t know without trying it. That would change the recipe and can’t guarantee the results.
Sarah
I burned mine :( 19 mins on 400. Was putting on low rack part of problem? I used wax paper cupcake holders- was that not a good idea? Is it better to put batter directly into pan?
Kate
Hi Sarah, I’m sorry to hear that! It depends on where it was to the heat source and wax paper isn’t meant to be heated.
Coco
These muffins sound so delicious! I was just wondering how many grams of flour 1 3/4 cups + 1 tsp would be. Thank you!
Cathy
These were a great consistency (used olive oil and maple syrup)! For the future, can you substitute 1:1 unbleached white flour for the wheat flour (or half and half)?
Thanks,
Cathy
★★★★★
Kate
Hi Cathy, I believe others have tried it and it’s worked well.
Michele Droll
I’ve made these several times with much success. I usually make double batches and share several with my sister and BIL who also really enjoy them. My daughter loves them! They are delicous using either maple syrup or honey! I like to use fat free Greek yogurt and find they rise up very nicely! For baking…..I will put them in the oven for the first 6 minutes at 425 to get a crunchier ‘bakery top’ and then I drop it to 390 to finish it out. I pull it out right at 16 minutes. They are perfectly moist! If giving as a gift– I will also pop an extra blueberry or two into any muffin that doesn’t have one showing through the top after I spoon it into the muffin tins. It looks so pretty aftewards to see the blueberry peaking out. Don’t forget the Turbinado sugar–that really finishes it!!
★★★★★
Linda
It’s the third time I’ve made blueberry muffins the first time they were lovely but these have sunk as soon as they’ve came out the oven. The only difference is I used low fat Greek yogurt the last time I used plain yogurt. Can you help please
Kat
Where do I start? The texture is amazing and my husband and friends couldn’t tell they were refined sugar free or white whole wheat. I love adding toasted walnuts and lemon zest to mine and even swap half the honey for date syrup occasionally. Oh, I failed to mention that I have made these muffins five times already and two were blackberry. Thank you for an amazing and healthy muffin recipe.
LAUREN
These were great! I made them with olive oil since I didn’t have coconut oil. I’ll definitely make them again.
★★★★★
Kate
Wonderful to hear, Lauren! I appreciate your review.
Emily
Have made these multiple times and love them. I want to make them again today but only have dark choc chips and no blueberries, could I substitute?
Also could I substitute self raising whole wheat flour for the regular flour and rising agents?
★★★★★
Kate
Hi! I haven’t tried it with this, sorry. I know chocolate chips work in my Maple-Sweetened Banana Muffins
Nidhi
I’m excited to make these! Do you think they will freeze well?
Kate
Hi! I believe these freeze well.
Elif Gunes
I love your recipes Kate!
It was my first time trying this one and I was a bit worried about how thick my final batter is and thought my muffins won’t rise! My worries are all gone now looking at the muffins from the oven window. Thank you very much it will be another fav recipe of yours at home!
★★★★★
New Baker
Loved your banana muffin recipe. I substituted oat flour instead of whole wheat and it turned out great. Can i do the same here??
★★★★★
Kate
Hi! I haven’t tried it, but you should. Just be sure to follow my oat flour post. I hope you love it!
Nadine
These are the best healthy blueberry muffins! I made them for my kids and I’m ashamed to say I ate the most! :) I will try more of your recipes. Thank you for this one!
★★★★★
Kate
You’re welcome, Nadine! I’m happy they were a hit.
Cindy
Delicious! I’ve been looking for a healthy-ish muffin that has a nice rise to it. These came out perfectly.
★★★★★
Kate
Wonderful, Cindy!
Lori
Love this healthier version of blueberry muffins. They taste great! Would never have thought to use extra virgin olive oil, but it worked well. Nice and moist muffins. The raw sugar on top adds the perfect amount of sweetness. Thank you for the recipe!
★★★★★
Carmen
Fantastic recipe! I used 1/2c oat flour because I was short on whole wheat flour and it turned out great. Not a sweet muffin which I appreciate.
★★★★★
K Mittendorf
Just made these – and they are delicious! I added a few extra blueberries as well. Also substituted a mix of allspice and ground cloves instead of cinnamon ( because of an allergy). Thanks for the recipe!
★★★★★
Anonymous
This was so good! I made mini-muffins because my pan isn’t as wide or deep as yours but still delicious :)
★★★★★
Jane
Can I substitute with Almond flour?
★★★★★
Kate
Hi Jane, sorry but I don’t find almond flour is a great 1:1 substitute.
Lakshmi
These came out absolutely amazing! Drizzled with a bit of honey on top and it is a decadent treat with zero guilt! Thanks for a great recipe, I am going to be coming back to us for sure!
Melisa
Delicious super moist muffins! Instead of regular flower, I used gluten free flower and they came out perfect!
★★★★★
Mary
These turned out perfect. Thank you for the recipe!
★★★★★
Y15M
Very tasty, just enough sweetness. I replaced blueberries with saskatooon berries and turned out good. Liked that these don’t taste like cake, but less sweetness and some fibre.
★★★★★
Jil
Love how these turned out! Going to be a breakfast staple for my toddler. I used fat free Icelandic yogurt because it’s what I had and they were definitely still moist.
★★★★★
Kristina Brangi
Do I use the same ratios if I want to make this a bread instead of the muffins? Does the cooking temp change? I’ve tried this a few times and it comes out on the drier side. Any suggestions? Thank you
★★★★★
Kate
Hi! I haven’t tried this as a loaf, sorry. I would check to see what others may have tried. It would likely need more baking time.
Diana
The blueberry muffins are so good! :-) I have made this recipe twice nice now since finding this recipe just a month ago and have also sent it to family members who are also anxious to try them.
thank you for this recipe, it is a keeper!
Katie
I made these muffins yesterday and my sons and I are enjoying them now for breakfast. They are sooo good! I’d make these again and again. I didn’t have wheat flour so I used regular. Need to pick up some at the store. Thanks for this wonderful recipe!!
★★★★★
Narinder
My muffins were slightly under baked I think slightly gooey in the middle rather than spongy what could I done wrong please?
Kate
Hi! I’m sorry you had issues with the recipe. Sounds like they needed more time. How long did you bake them for?
Leily
I made these with spelt flour and they still tasted amazing. My kids love them! I’ve tried a few of your recipes and they’re all amazing. Thank you!
★★★★★
Kate
You’re welcome, Leily!