These healthy blueberry muffins are high in protein and low in sugar, making them a perfect option for breakfast on-the-go!
Made with just a few pantry staples and ready in under 20 minutes - you can't beat this recipe for a healthy take on a household favorite snack!
For a Dairy Free Blueberry Muffin option, click here!

Gluten Free Blueberry Muffins
These healthy blueberry muffins are packed with superfood ingredients, high in protein, and low in sugar, making them a perfect option for breakfast on-the-go!
They are naturally gluten-free (made from oat flour) and sweetened naturally with a touch of honey and some applesauce. Plus, they are super simple to make!
Oh, and did I mention they take LESS THAN 20 MINUTES?! Including baking time. So, no excuses that you're "too busy".
How to make the Easiest Bluberry Muffins Ever
Add all the wet ingredients to a bowl and whisk, whisk, whisk! Then, gently fold in the wet ingredients.
Add a swirl of blueberries on top (or not, its really up to you).
Spoon the batter into a muffin tin. Use a Cookie Scoop to mitigate mess and ensure even-size muffins.
Pop immediately into the oven, and in less than 30 minutes you have these!
Fresh, warm, sweet-but-not-overly-sweet, bursting-with-juice-blueberry-goodness muffins!

Ingredients in Healthy Blueberry Muffins
Thanks to the superfood ingredients like juicy blueberries, Greek yogurt, honey, eggs, and the applesauce, these healthy blueberry muffins are pretty moist. Add some oat flour to thicken up the batter, and you've got the easiest gluten free muffin recipe ever!
Each ingredient is packed with health benefits and delivers nutritionally.
Blueberries are packed with antioxidants and fiber.
Honey is also rich in antioxidants, and is antibacterial and can help with digestion.
Applesauce is a good source of fiber and Vitamin C. It also contains polyphenols, which may help to reduce blood pressure
Greek Yogurt adds a serious amount of protein, keeping you full and satisfied for longer. For a Dairy Free Blueberry Muffin recipe, you can add more applesauce in place of the Greek Yogurt
Oats contain tons of soluble fiber, help control blood sugar levels, and can even help lower cholesterol.
Plus, did I mention that all the ingredients in these muffins are naturally gluten free, and refined sugar free?

What if I don't have Blueberries?
Don't panic!
You can easily sub the Blueberries in this recipe for your favorite berry. I've had success with deliciously sweet Blackberries during peak summer season.
If you really want a sweet treat, you could even replace the berries with chocolate chips. Hello, Gluten Free Chocolate Chip Muffin recipe!
If you want to use a totally different fruit, like banana, I'd recommend using a Banana Recipe like this one.

Blueberry Jam Topping
Adding the blueberry "jam" on top of these delicious blueberry muffins ensures that every muffin has plenty of blueberry goodness. Plus adds aesthetic appeal, aka makes them pretty, in my opinion.
To make it, I simply microwaved some frozen blueberries and gently smashed them with the back a fork and a dash of honey.
You can do this with fresh blueberries and/or on the stove top too. Or, simply use store-bought blueberry jam! (I would just look for one that is not loaded with a ton of added sugars).
If you want to skip this step, you totally can. But it makes these muffins extra moist and feel a touch fancier than your average everyday blueberry muffin. Chef's choice!

More Gluten Free Berry Recipes
If you like blueberries in your baked goods, check out some of these other recipes:
- Blueberry Lemon Breakfast Bread (which you can make into muffins!
- The Healthiest Fluffiest Blueberry Pancakes
- Healthy Berry Cinnamon Coffee Cake
- Paleo Banana Blueberry Pumpkin Seed Loaf
Take me to the Archive of berry recipes!
For a Dairy Free Blueberry Muffin (with a refined sugar free streusal topping) option, click here!
Did you make this recipe?
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Healthy Blueberry Muffins
These healthy blueberry muffins are high in protein and low in sugar. They are gluten-free, and sweetened naturally with a touch of honey and some applesauce.
Ingredients
Dry Ingredients
- 2 Cup Oat Flour (or ground up oats)
- 2 teaspoon baking powder
- ½ teaspoon salt
- ½ teaspoon cinnamon (optional)
- 1 Cup Blueberries, fresh or frozen
Wet Ingredients
- ⅓ C Applesauce (Sub: Neutral oil or more Greek Yogurt)
- ⅔ C Greek Yogurt (Sub: More Applesauce, or vegan yogurt)
- ⅓ - ⅔ C Honey (Add more for sweeter muffins)
- 2 Eggs (Sub: Vegan Flax Eggs)
For the jam on top (OR, use store-bought blueberry jam):
- ½ Cup Blueberries, fresh or frozen
- Optional: dash of cinnamon, honey
Instructions
- Preheat oven to 400 and line/grease a 12-muffin tin.
- In a large bowl, combine all the wet ingredients. Then, fold in the dry ingredients, except the blueberries.
- Meanwhile, make your jam topping:
In the microwave: microwave the blueberries in a bowl for ~30 seconds. Add a dash of cinnamon and salt. Gently bash with the back of your fork.
-Or-
On the stove: Warm the blueberries over low-medium heat for ~10 minutes until berries start to melt and blister. Add a dash of honey (~1tsp) and some cinnamon and bring off the heat to cool.
-Or-
Use your favorite storebought blueberry jam. - Lastly, gently fold the blueberries into the muffin mix until just combined. Scoop into muffin liners. Top each muffin with a spoonful of the jam. Use your fork to spread it in a swirl, if you want.
- Bake for 15 – 17 minutes. Let cool and enjoy your healthy blueberry muffins! Store in fridge for 4 – 5 days, or freezer for up to a month.
Notes
Use a cookie scoop to ensure even size muffins and help get that beautiful dome-top.
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Kalie
Can I substitute the oat flour with white flour?
Btw I really like the idea of using applesauce. Is it unsweetened or sweetened applesauce?
thegranoladiaries
Thank you! I would use unsweetened applesauce to keep the recipe low sugar. I haven't tried this with white flour, but it should work, it will just no longer be gluten free!
Christina
These look amazing!! Do you think we can use flax eggs to replace the regular eggs?
thegranoladiaries
Absolutely!
Niki
This was so yummy! super easy to make and really healthy. i would def use this base for other recipes- substitute the blueberries for strawberries or chocolate chips. i'll be making these weekly. THANKS! 🙂
thegranoladiaries
I'm so glad you liked it! Sounds delicious with strawberries and chocolate chips!!
Cindy
Can this recipe be made with a cake pan instead of muffin tins?
thegranoladiaries
Yes that should work! You may just need to bake for 5-10 minutes longer. Keep an eye on it to make sure it doesn’t burn though!
Hillary
Love these muffins! I added a few modifications to my taste: 1 -2 tsp vanilla to batter, make blueberry jam on stove top with 3tbs maple syrup, 1 tbs chia seed and lemon zest. at the end with blueberries fold in about 1/2 finely chopped almonds. creates amazing texture and crunch!
Is it ok to try with gluten free flour instead of oat flour
There delicious , but I will also be trying to use strawberry's and chocolate chip also . Thanks for the receipe
thegranoladiaries
That is such a great idea! Strawberry muffins and chocolate chip muffins sound great!
Whit
There is no water?
thegranoladiaries
Hi Whit, are you expecting water?
Kameron
Just made my first batch! My kids can’t wait. Do you think I could fold the blueberries in the batter instead of making it a jam topping?
thegranoladiaries
That's great! Hope your kids love them! Yes, you can fold them in and now make the jam topping - or you could do both, or either one, depending how prominent you want the blueberries to be!
Gina
Will these work as mini muffins?
thegranoladiaries
Hi Gina, yes these will work as mini muffins. Make sure to reduce the cooking time and keep an eye on them though, as they will bake faster by probably 5 - 10 minutes!
Veena Azmanov
These Muffins are surely a treat. Love the Blueberry toppings and the healthy version to making these yummy and delicious.
thegranoladiaries
So glad you like them, Veena!
Stephanie
I just made these muffins. I'm not a honey fan, so I used just shy of 1/3c of pure maple syrup, added a splash of vanilla and these are absolutely delicious! Thank you for this delicious recipe
Sara
Can you sub the oat flour with almond flour?
Nicole
I did and they turned out great!
Krissy Allori
These are amazing. I really enjoyed them and didn't feel the guilt I do with some other muffins.
thegranoladiaries
That's awesome! Glad you enjoyed them!
Krystal
Could you add protein powder to this to give it some staying power?
thegranoladiaries
Probably! I haven’t tried it but I think it should work. You might want to add 1/4 cup more liquid as well so it doesn’t dry out. If you try it, let me know!
Anjali
These blueberry muffins were like little bites of heaven!! I love how healthy they are - they made for an awesome grab and go breakfast for me and my kids!
thegranoladiaries
Yes! Such a good and healthy breakfast on the go option!
Megan
Would I be able to use all purpose gluten free flour with the same ratio as the oat flour?
thegranoladiaries
Yes that should work beautifully!
Terri
I love these blueberry muffins - so healthy AND delicious~!
thegranoladiaries
Thanks so much, Terri! Glad you love them!
Lisalia
YUM so beautiful to look at and even better to eat! I have to confess mine were less than healthy because I added BUTTER on top hahaha. But So so so so good! Thanks for this yummy recipe!
thegranoladiaries
Adding butter is always a good idea!
Momoko
Hi, what can you substitute applesauce with?
thegranoladiaries
Hi! You can use Greek yogurt, or any neutral oil instead of applesauce!
LeAnna
Did you post the nutritional information? Maybe I missed it.
thegranoladiaries
Not yet! I will hopefully get around to adding that on all my posts in due time!
Cris
What do you suggest as a replacement for the Greek yogurt to make these dairy free?
thegranoladiaries
Hi Cris, you can use Vegan yogurt, or I have a dairy free option linked at the top of this post!
Cathers
This looks and sounds great! Pinned to try later 🙂
Ashley
I love these muffins! I have made them twice so far! I’m curious how I would modify this recipe for lemon poppyseed. I’m nervous modifying your recipe so any advice would be greatly appreciated!!
thegranoladiaries
I'm so glad you like them, Ashley! I have another recipe on the site for a Gluten Free Lemon Poppy Seed Muffin made with oat flour, that may be better than trying to modify this one:)
ABM
I was getting bored of my ususal breakfast and these were really easy to make and delicious. We had some freshly homae-made blueberry jam and these muffins went perfectly with them.
Carrie
I made these today but they came out really dense. Wondering what I did wrong. I used all Greek yogurt so no oil or applesauce.
thegranoladiaries
Both the oil and applesauce really lighten up the batter so its definitely possible omitting them made the muffins denser. Also overmixing the oat flour and Greek yogurt or letting the batter sit for too long would cause the oat flour to absorb a lot of the yogurt and become very heavy.
Jeanne Williams
Loved these! What is the calorie count, protein, fat??
thegranoladiaries
It should be at the bottom of the recipe card!
Rachel
Hi! Could I use Gf flour instead of oat flour?
thegranoladiaries
Sure can!
Lisa
I couldn’t find the nutrition information on these. Is it available? Thanks in advance!!
thegranoladiaries
Not yet but I plan to add it in for all my recipes at some point!
April
Can you sub mashed banana for applesauce?
Casandra
Hey there! can I make these with coconut flour??
Sheryl
This is a 5-star recipe! It is just spectacular and yummy! Thank you for sharing this recipe. It turned out so well. I make these again and again!
Carol
Do you know calories on these? They sound awesome!
Ashley
The taste is so good! Perfect sweetness and much healthier than the ones we bought in stores for our kids!
However they’re very dense and a little rubbery. They’re also sticking to the cupcake liners. We used old fashioned oats to make our own flour. Other than that we followed the recipe exactly how it’s written. Any suggestions for next time?
thegranoladiaries
I'm glad you like the taste!
For sticking to the liner, make sure you are spraying your muffin liners with oil, since there isn't a lot of oil in the muffins, they will stick otherwise!
For the rubbery texture, that can often happen from overmixing. Make sure you mix the batter gently and JUST until combined, and then pour it out.
Let me know if these tips work for next time!
Tracy
Do you use 2 teaspoons of baking powder or 2 tablespoons?
Debbie
Made these and love them! Please provide nutritional info.