Healthy Blueberry Muffins made with whole wheat flour, maple syrup and applesauce are fluffy, moist, and absolutely delicious! Make ahead or eat fresh out of the oven for a nutritious breakfast or snack.
Healthy muffin recipes are easy to make, so double these and freeze some for later. Other favorites include these almond flour blueberry muffins and healthy blueberry bread.
Table of contents
These healthy blueberry muffins come out fantastic every time. With no refined sugar and nutrient dense ingredients, I can feel good about feeding these to my family.
Moist, light and so fluffy, both kids and husbands love these and healthy strawberry muffins! They are perfect right out of the oven and leftovers are perfect for healthy snacks.
Usually, I prefer to eat my berries fresh, like on this healthy french toast casserole or served with Ukrainian sweet lazy pierogi. However, these blueberry muffins deserve even the priciest supermarket January blueberries!
I recommend to buy organic whenever you can because berries are on a Dirty Dozen list. And if you can’t find fresh, frozen work too, just like in blueberry oatmeal crumble bars!
What Makes These Blueberry Muffins Healthy?
- Whole grain flour: By using 100% whole wheat or spelt flour these muffins are full of nutrients plus fiber.
- Naturally sweetened: Skip the refined white sugar, these muffins use maple syrup or honey which means less sugar overall than your giant coffee shop muffins.
- Low oil: Unsweetened applesauce not only keeps these muffins moist, it lowers the use of heavy oils for lighter, better for you blueberry muffin!
Ingredients You Will Need
My healthy blueberry muffins recipe contains simple ingredients:
- Whole wheat or spelt flour: Baking is a science and it’s best to use whole wheat or spelt flour only for this recipe. Using all purpose or gluten free flour will need adjusting the recipe and I haven’t tried. Whole wheat pastry flour or white whole wheat may work, if you try, please let me know.
- Blueberries: My favorite homemade blueberry muffins are with fresh blueberries but frozen blueberries can be used with great success.
- Applesauce: I use unsweetened applesauce but if sweetened is all you can find, that works. Your muffin will just be sweeter. Here is a great Instant Pot applesauce recipe as well.
- Eggs: Provide lift and binding, see recipe notes for egg free.
- Any oil: Healthy widely available options extra virgin olive oil, avocado oil, coconut oil (melted first).
- Liquid sweetener: Maple syrup or honey. Please do not use any dry sweetener. It will throw off batter consistency and recipe will not work.
- Vanilla extract: Pure, not imitation for best taste.
- Cinnamon: Adds a warm taste and light spice to the muffins.
- Baking staples: Baking powder, baking soda, and salt.
How to Make Healthy Blueberry Muffins
Easy to make in one bowl, you may want to double this healthy blueberry muffin recipe to always have a wholesome healthy breakfast on hand for your own family!
Combine liquids and leavening agents first by whisking them well in a large mixing bowl. Ensure your baking powder and soda have completely dissolved.
Then add flour and stir gently to mix. Do not over mix your batter as additional gluten will develop and result in dense muffins.
A few patches of flour are OK and better than perfectly smooth batter. You can also let it sit for 3 minutes or so to absorb moisture. Then give 1-2 final stirs.
Add blueberries and give a few stirs just enough to incorporate into the muffin batter.
Fill muffin tin using large ice cream scoop with your muffin batter. Bake for 22 minutes or until toothpick inserted in the middle comes out clean.
Cool in the tin for 30 minutes before transferring onto a cooling rack to cool more or enjoying.
Tips for Best Results
- Mix batter only until combined. Stir a few times and let batter sit for a few seconds to let flour absorb the moisture. Stir again. A few flour patches here and there are fine.
- Keep an eye on muffins while they bake. All ovens vary and I recommend to check your muffins 3 minutes to the end. If toothpick comes out clean, time to remove muffins. They keep cooking with residual heat in a tin.
- Let muffins cool completely. These blueberry muffins are delicate, light, and fluffy. If you don’t let them cool patiently for 30 minutes, they will deform and fall apart a bit.
- Mini muffins: You can make mini muffins and bake for 11-13 minutes. Do toothpick test. You might also love to make these healthy blueberry pancakes!
Can I Use Frozen Blueberries?
Yes. Frozen berries are a great way to make healthy blueberry muffins during cooler months. No need to thaw the frozen blueberries.
However, if you are worried about them turning your batter blue, rinse them a few times under cold water, then gently pat dry. Fold them gently into your muffin batter and give a few stirs. Once you notice some blueberry streaks stop stirring to prevent further bleeding.
In this recipe, you cannot substitute any other flour except for whole wheat flour and spelt flour. Try these almond flour blueberry muffins or healthy blueberry breakfast cake for gluten-free options.
Yes, to make these muffins egg free and also vegan, you can use an equivalent amount of flax egg or chia seed egg.
Yes. You can use an equal amount of plain regular yogurt or Greek yogurt like I do in healthy blueberry banana muffins or healthy lemon blueberry muffins.
I did not find blueberries sinking to the bottom of muffins. If you do, next time toss them with 1 tbsp of flour in a separate bowl before adding to batter.
What Can I Serve These Muffins With?
Make healthy fruit salad while waiting for your muffins to cool off. It goes great with fresh baked muffins!
Or spread some peanut butter or cream cheese on top.
Quinoa breakfast bake, a side of breakfast potatoes, healthy baked apples, and egg muffins would all be great for a light lunch or brunch spread in addition to these muffins.
How to Store and Freeze
To store: These won’t last more than 2 days because they are so good! Store muffins in an airtight container placed in a cool dry place for 3-4 days or in the fridge up to a week.
Freeze muffins: Bake and cool muffins completely. Then arrange them in a single layer in resealable plastic bag or any container with a lid. Freeze for up to 3 months.
To reheat: Thaw on a counter for a few hours. Warm up in the oven at 350 F or microwave for 30 seconds for that freshly baked experience.
Enjoy these healthy blueberry muffins! Would love to know if your kids approved!
More Healthy Muffin Recipes
- Healthy banana muffins
- Almond muffins with berries
- Healthy morning glory muffins
- Healthy chocolate chip muffins
- Healthy apple muffins
And if you love a good healthy pie, check out this gluten free blueberry pie.
Healthy Blueberry Muffins
- 2 large eggs
- 1 cup applesauce unsweetened
- 1/2 cup maple syrup or honey
- 1/3 cup avocado oil or coconut oil melted
- 1 tsp pure vanilla extract
- 1 tsp cinnamon
- 2 tsp baking powder
- 1/2 tsp baking soda
- 1/4 tsp salt
- 2 1/3 cups spelt or whole wheat flour plus 1 tbsp for dusting
- 1 1/2 cups blueberries fresh or frozen
- Preheat oven to 425 degrees F and line muffin tin with unbleached muffin liners or use silicone muffin tin (I used both and didn't spray anything).
- In a large mixing bowl, add eggs, applesauce, maple syrup, oil, vanilla, cinnamon, baking powder, baking soda, and salt. Whisk well to combine, making sure baking powder and soda have dissolved. Add flour and stir gently to mix. Do not over mix.
- In a small bowl, toss blueberries with 1 tbsp flour, add to the batter and give a few stirs.
- Using large ice cream scoop, fill 12 openings with batter. Bake for 10 minutes, reduce oven temperature to 375 degrees F, and bake for another 10 minutes or until toothpick inserted in the middle comes out clean.
- Remove from the oven and let muffins cool in the tin for at least 30 minutes before transferring onto a cooling rack to cool more or enjoy.
- Store: Store in an airtight container in a cool dry place for up to 3 – 4 days or in a fridge for up to a week.
- Freeze: Bake and cool muffins completely. Arrange in a single layer in resealable plastic bag or any container with a lid. Freeze for up to 3 months.
- A: You can use equal amount of plain regular or Greek yogurt to replace applesauce.
- Gluten-free? Unfortunately only flours that will work in this recipe are the ones listed.
- Do not overmix batter: Stir a few times, let batter sit and stir again. A few dry flour patches are fine.
- Egg free: Learn how to make a flax egg or chia seed egg.
Hi, I noticed that you mentioned yogurt in your notes, but I didn’t see any yogurt listed in the ingredients or the directions. Just curious if it was accidentally left out?
You can use equal amount of plain regular or Greek yogurt to replace applesauce, if you wish. Sorry, fixed that.:)
Such an awesome recipe. Along with the blueberries I added Frozen cherries, unsweetened coconut and walnuts. Yum
Sounds like a delicious loaded muffin!
Thanks for the great recipe. Much better than the ones from a box.
Thanks for the rating and review!
These are my family’s favourite blueberry muffins of all time and have been for quite awhile! So fluffy & perfect.
I did notice that you changed the recipe and increased the amount of sweetener, oil, and flour, and I’m just curious as to why? And won’t it now make more than 12 muffins?
The amounts for the ingredients are correct as listed and will make 12. But feel free to use 1/3 c maple syrup, 1/4 cup oil, 2 cups flour if you wish.
These are fantastic! For people asking about gluten free, I’ve made 4 dozen now using King Arthur’s Measure for Measure and following the recipe exactly otherwise. I’d recommend weighing the flour (280g). They have turned out so well gluten free. I can only imagine how wonderful the gluten versions must be. Thank you!
Thanks for letting us know Becca! So glad it turned out well for you!
I haven’t tried this yet, but just wanted to say thank you! For one, so much information and such details makes your recipes fool proof. And, such varieties! For another, you do indicate if substitutions can be made and offer alternatives. I had bookmarked a TON of recipes and recipe sites because I need gluten and sugar free. Now, I will only go to your website, plus I have your recipes delivered to my inbox as well. No more searching for recipes that I can make and eat! And no more compromising on taste. Thank you dear Olena!
So glad you have found it all so helpful Lori! Glad to have you here!
Hi, if i make these blueberry muffins mini how long do i cook them for? and at the same temperature?
Yes I would do 5 at the higher temp, then 3 min at lower temp, check, then 2 min more etc until toothpick test indicates done.