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
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
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 already know that I love your recipes :). I prepared these today and they turned out amazing!
Genuinely the best muffins i’ve ever made! I made them last week, and had one everyday for breakfast. Just made them again tonight for another round. Perfect fluffiness, texture and flavour. Love them!
These are so good! I love that they’re not too sweet and the texture is great. I used the coconut oil, extra cinnamon and extra blueberries. My silicone cupcake and mini bundt cake molds worked great, popped right out. My sister also made these today and both her and my brother-in-law love them. We will definitely make these again. Next time I’m going to try using my unsweetened homemade applesauce in place of the oil. Excited to experiment with these. Thanks for the recipe!
These are by far the best blueberry muffins ever. I use Cocojune vanilla chamomile yogurt which is the creamiest coconut yogurt. My husband loves these fresh from the oven while the tops are a little crispy. I make a dozen at a time. Is it possible to make an entire batch and keep the batter in the fridge while baking a few at a time?
can i replace with all purpose flour?
I love these so much! I’ve made them weekly for a month now because my family enjoys them so much. They’re so easy and quick and are a perfect little snack before breakfast or on the way home from a hike. And bonus: I usually have all these ingredients on hand for a sudden blueberry muffin craving.
Can oat flour be used instead?
Hi Lois, I haven’t tested with oat flour, but if you do, please share how it turned out!
Can you use apf?
Hello Katie,
Yes, you can use all purpose flour.
Hi! I’ve made these several times and they’ve been delicious! I made them last night- same ingredients and they’re always great turned out so dry and a little hard. Any guesses? Did I over bake?
Hi Stefani, I’m sorry these didn’t turn out this time. Over-mixing or over-baking can make them dryer and harder. I hope this helps.
These muffins came out soft and moist. I didn’t have any white whole wheat, so I made the recipe with whole wheat pastry flour, and they were great! Thanks!
I don’t have any yogurt, is there something I could use instead?
Hi Noelle, you could use sour cream instead.
My favorite blueberry muffins! They are in heavy rotation at our house. Perfect with a cup of tea!
This is a great recipe, thank you! Is it possible to make it into a bread instead?
These are my favorite muffins to make and keep on hand for visitors! I make two times the recipe and use a silicone muffin pan. I love all your recipes.
These are our family’s favourite muffins. Thanks for providing us with great recipes.
Where can I buy white whole wheat?
Hi Mary, King Arthur Baking and Whole Foods 365 brand both carry it — there may be others, but a larger speciality grocery store or a health goods grocery store will likely have it in stock. You can also order online.
Love this, they came out so fluffly and delicious. this is in my regular baking every week! My family loves them.
My family loved these muffins! Maple syrup and coconut oil were a perfect combination – not too sweet, not too buttery. Very fluffy muffins too! I’m from Finland and we rarely use vanilla extract here, so I used vanilla sugar instead. Thank you for the recipe!
Hi there! I love blueberry muffins, so thank you for the recipe. Question: Can I substitute almond flour for whole wheat or gluten-free whole wheat flour?
Hi Irma, it would require several adjustments since the flour in this recipe absorbs the fat of the butter in a way that almond flour would not. I haven’t tested it. I have modified my banana muffin and loaf bread for almond flour, and I wrote detailed explanations as to why I amde the adjustements, if you want to give it a try with this recipe https://sooka.info/gluten-free-banana-bread-recipe/%3C/a%3E%3C/p%3E
Good day, Kate,
Thank you so much for responding to my question. I will make according to the ingredients noted. Best, Irma
Can this recipe be backed in a cake pan? I love your recipes!!
Hi Bobbie, other commenters have said they’ve had success with baking in a cake pan instead of muffin tin but I haven’t tested it. A loaf pan works better than a round cake pan. You will need to adjust the bake time as it will need more time, and perhaps lower the temperature to 350F. I would watch it closely and test to make sure it is cooked all the way through. If you try it out please share the results!
I baked in a loaf pan at 350 for 1 hour and it was perfect!
Thank you for your recipe. The muffins are truly very nice, not dry, rose well & look & taste yum. I used liquid honey, half wholemeal flour & half high grade flour & 1 tsp vanilla. 16 minutes cooking was just right. Will make again – soon!
I find using frozen wild blueberries, they’re much smaller, spreads the berries out more evenly.
I made a cake instead of muffins with same ingredients. It tasted fabulous. Everyone loved it. It was super moist and busted with blueberries flavor. Thank you.
So glad that worked for you! Thanks for sharing.
Could I use almond milk in place of the yogurt? Or is there any other substitution I could use?
Hi Brittany, I recommend the recipe as written. Yogurt contributes to the leavening of the muffins, and has a tang that almond milk doesn’t. If you do substitute almond milk, it will result in a denser crumb. If you need to make it vegan, my recommendations are to replace the yogurt with a smaller amount of vegan buttermilk—just mix ⅔ cup non-dairy milk with 2 teaspoons vinegar. Let it rest for 5 minutes before adding it to the other liquid ingredients. Or, use 1 cup vegan yogurt. The notes have other modifications I suggest.
Love these. Our mornings start with a blueberry muffin with 1st cup of coffee. A delicious habit. Always bring them to grandkids. I make regular & mini sizes. Thank you for sharing❣️
So glad you enjoyed!
Looks yummy. Have you tried this recipes as a loaf?
If so what size loaf pan and how long did you bake it?
Thank you for the recipe, I always enjoyed the Jordan Marsh Muffins!
This is my go to muffin recipe because I almost always have frozen blueberries on hand.
Today I had the ‘brilliant’ idea to use the batter to make mini donut muffins for my preschooler. I forgot that muffins rose though, so the top half looked like a perfect muffin while the bottom looked like a donut.
Fail?
Nah. It’s a half muffin-donut. And my daughter finds it hilarious.
Can this be made with freshly milled flour? Any modifications needed?
Hi Natasha, I haven’t tested it, but you might need modifications depending on the type of wheat. Sometimes the amount of flour needs to be increased, and sometimes the hydration needs to be adjusted in the recipe. If you try, I’d love to hear the results!
Wondering this also, and which grain you would use. did you test it out?
Hi there. Thanks for this delish muffin recipe. I did mine with 1c whole wheat flour, 1/4c flaxseed mead, and 1/4c coconut flour, plus additional 1/2t of baking soda. Used 1/3c of honey instead of 1/2c and turned out still sweet and puffed up. Love them!!! Will next time try decreasing the whole wheat flour and substituting whey protein powder and ground chia seeds for the whole wheat flour to make it protein-packed, low-carb, high-fiber.
Delicious! I made these with coconut oil and maple syrup. Used organic whole wheat flour and fresh picked blueberries. Thank you for this recipe. Just what I wanted. Healthy and easy to make.
Thank you for the recipe! How much could I reduce the sweetener without harming the structure/texture of the muffin?
Hi Aidan, I think the recipe as written is balanced and sweet enough without being two sweet. Many share their modifications to suit their taste in the comments which could give you some ideas.
curious if i could use melted butter instead if oil?
Hi Aly, you could try it. Oil tends to produce a more moist and tender crumb and helps the muffins stay moist longer.
Made it already twice. Everybody was very happy! Used raw sugar instead of honey. Just need to warm the muffin for 10 seconds, if are kept at fridge.
Can you freeze?
Can I halve this recipe?
Hi Gillian, you could certainly half it, but some of the measurements are a bit tricky. I’d recommend making the full batch and freezing half of them. They reheat very well.
Delicious recipe! I used whole wheat flour before for making other muffins and I didn’t like the texture. But this recipe was fluffy! I also used maple syrup and it was the right amount of sweetness. I will definitely make this again!
These muffins are the WORST I have ever made – I repeat, WORST muffins I have ever made!!! The muffins were burnt, PLEASE lower the temperature when cooking it, if you even do which I DO NOT RECOMMEND. This tasted like vegitable juice, basically terrible. Would never make again if I had the choice to do it again or die.
Can the batter be made the night before and refrigerated before baking?
Hi Sabrina, I haven’t tested it, but if you do, I recommend keeping the fruit separate and mixing in just before baking so it doesn’t releast extra liquid, and you should ensure you are using a double-acting baking powder, as aluminum-free baking powders may not work as effectively when refrigerated.
Should greek yogurt be at room temp too or is it just the eggs?
I’m making them for this mother’s day!
It’s important that the eggs be room temperature so they distribute easily through the batter and form an emulsion. This is less important for the greek yogurt.
Hi! I varied this recipe a bit, by dividing the flour into 1/2 organic oat flour & 1/2 organic unbleached almond flour; added some coursely chopped walnuts & I used coconut sugar on the tops.
It makes delicious muffins!
I had first thought maybe they weren’t done, but they were fine. Very moist & healthy…..we love them!
Thank you!❤️
Great recipe! I omitted the turbinado sugar and blueberries. I cut the muffins in horizontal slices and used that for the “cake” part of our strawberry shortcake. It was delicious! This was my first time making this recipe, but next time I will try my hand at an 8×8 pan – just for the cake aesthetics, though!
Hi, I love this muffin recipe! It’s a favorite among my family, and I love knowing it has healthy ingredients and does not use a cup or more of sugar like the typical muffin recipe. Question? Could I substitute rhubarb in this recipe? I have a massive plant and can’t find any healthy recipes for rhubarb muffins.
Hi Bridget, I’m so glad you like it. I haven’t tested with rhubarb, but I do have a few recipes that feature rhubarb.
I don’t have coconut oil, but I do have olive oil. However, I’m having a bit of an aversion to olive oil lately, does it have an impact on the taste? Or you don’t taste it?
Hello, olive oil will impact flavor of baked goods. I prefer the recipe as written, but you could substitute a neutral flavor oil like vegetable or canola.
How would this recipe work if I added some mashed bananas. I only trust Cookie and Kate muffin recipes =)
Hi Marjan, if you are looking for banana muffins, try this recipe.
This is my go to muffin recipe for my whole family! We come back to them time and time again. Love making them at the beginning of the week for an easy kid breakfast. Most recently I added lemon zest- delicious!
These muffins were outstanding! Most WW baked goods are so dense and dry. These were heavenly! Will make again! Rounded so beautifully on top.
Hi, I’m out of coconut oil and worried extra virgin olive oil is gonna make muffins taste weird. Can I use melted butter instead?
I really enjoy these delicious and healthy blueberry muffins. I have made them several times and the recipe comes out the same amazing way every time! Thank you so much for what you do. It makes my world more delicious!
Hi Kate, your ingredients are measured by cup, could you tell me please what the measurements are in grams.
I so want to try the blueberry muffin recipe.
Thankyou
Regards
Barbara
Hi Barbara, thank you for the suggestion. I have a long term goal of updating my baked good recipes to include measurements in weight.
Thankyou for your reply, j actually made those blueberry muffins, using the cup measurements, they turned out sooo yummy.
(I was given as a gift cup measurements; whole cup, half cup etc.
So i gave it a go
Hi Barbara, I’m so glad it worked for you!
These are delish! Made them on a whim and used olive oil, mix of honey and maple syrup, and the vegan alternative to yogurt cause I didn’t have Greek yogurt. Delicious!! Fluffy and with a rich earthy flavor. My kiddo and I are devouring them! Thanks!
My coconut oil says heat up to 350 degrees. Is that fine to use with this recipe at 400 degrees?
Hi Jenny, coconut oil is fine to use in baked goods. The directions you reference refer to frying or sautéing. Coconut oil has a slightly higher smoke point than olive oil, for example, so can be used to cook at higher temperatures than olive oil.
Do these freeze well? Keen to try for lunch boxes
These are great for freezing. If you put them in a lunch box straight from the freezer in the morning they will be ready by lunchtime.
I love making these muffins! they are the best for school lunches or just for an on the go snack!
Thank you so much!!
Hey there, I have been recently diagnosed with LADA (Autoimmune Type 1 diabetes.) I already have your cookbook and cook healthy. (thank you! ) I am messing around with the recipe, not sure of the nutrition so I will leave that for someone else to figure out:)
What I can tell you is that I used 3/4 cup almond flour and King Arthur Golden Wheat (1 cup.) Otherwise the same except I subbed almond extract for vanilla and zero % FAGE yogurt. 1 small muffin pared with 2 scrambled eggs did not spike the blood sugar! Success! Obviously, this is one diabetic’s experience. Each of us is different and I am not suggesting this will work for anyone but me. I will continue to practice and tweak, probably with sugar substitutes although they don’t sit well on my tummy. thank for a lovely recipe!
These blueberry muffins were fantastic…They came together so easy, very good!!
Ahem–HOMEMADE Greek yogurt can indeed pass for sour cream on a taco. ;-)
Thanks, Kate!
5 STARS, but I changed recipe a bit.
Fantastic muffins
I replaced 1/2 cup of whole wheat flour with keto whole wheat for more protein.
Added a bit more honey – because I had a small amount left and I just used it all.
Added a tbsp of ground flax seed
I used one 5.5 ounce (personal size) container of Greek vanilla flavor yogurt and one 5.5 ounce regular Greek yogurt because that’s what I had. The two 5.5 ounce containers basically measured to one cup with a wee extra. It was great.
These muffins were FANTASTIC!!!
I did top with plenty of turbinado sugar for the glistening crunch, which didn’t disappoint.