Healthy Almond Flour Blueberry Muffins are tender, fluffy and naturally gluten free! Made with almond flour, Greek yogurt, and sweetened with maple syrup they are perfect for a grab and go breakfast or snack.

These aren’t the first almond flour muffins I’ve shared. Almond flour zucchini muffins and almond flour pumpkin muffins are a few of our favorites!

Three healthy almond flour blueberry muffins stacked on top of each other.

Considering my love for almond flour muffins and blueberries, I’m surprised this recipe hasn’t come sooner. Inspired by my healthy blueberry muffins and almond muffins with berries, I’ve created 100% almond flour muffins with blueberries!

They are naturally gluten free blueberry muffins that are also refined sugar free, oil free, and grain free.

The addition of almond flour helps yield a super moist and hearty blueberry muffin recipe that the entire family will love. They might even request them for dessert with a scoop of vegan vanilla ice cream!

I’ve spent a lot of time perfecting my baking with almond flour including healthy pumpkin cake, almond flour banana bread, even an almond flour skillet cookie and Instant Pot peach cobbler.

Finally, you can enjoy a muffin without any of the “empty calorie” ingredients of many store bought options, perfect for nourishing your body while giving you a treat!

You may also love these 21 healthy muffin recipes!

Healthy almond flour blueberry muffins in a blue muffin tin.

Why You’ll Love This Recipe

  • Suitable for many dietary preferences including gluten free, low sugar, and high protein.
  • Almond flour is higher in protein, healthy fats, vitamins, and minerals.
  • These muffins require just 10 ingredients and are ready in 30 minutes.
  • Yields light, fluffy, moist, and fruity muffins.
  • Enjoy immediately or freeze for up to 3 months.

It’s like eating healthy blueberry breakfast cake anytime of the day!

Ingredients in Almond Flour Blueberry Muffins

Almond flour, Greek yogurt, maple syrup, baking powder, baking soda, blueberries, eggs, orange, vanilla, cooking spray, salt.

With only a few nutrient dense, real food ingredients these muffins are bursting with light nutty taste and fresh blueberries!

  • Almond flour: Superfine blanched almond flour is best. Coarse almond flour and almond meal should work but will have a slightly denser texture. You can buy it or here is quick tutorial how to make almond flour at home.
  • Blueberries: You can use fresh or frozen blueberries.
  • Eggs: You’ll need 3 large eggs.
  • Sweetener: Maple syrup and honey are my favorite options, though most liquid sweeteners should work. Liquid sugar free options (like liquid stevia) may also work, but I haven’t tried.
  • Greek Yogurt: This helps to add fat and moisture to the muffins. Use 2% fat or higher for best results.
  • Baking powder and baking soda: These leavening agents provide lift and fluffy texture to the muffins.
  • Salt: All you need is a pinch to balance and enhance the overall flavor.
  • Vanilla extract: Use natural extract or paste for the best results.  
  • Citrus zest: While this is technically optional, I recommend adding it for extra flavor. You can use lemon or orange zest.
  • Misto: Or cooking spray for your muffin tin and liners.

Step by Step Instructions

Parchment lined muffin tin.

Prepare the muffin pan: First, preheat the oven to 350 degrees F and then line a 12-muffin tin with parchment paper muffin liners sprayed with a bit of cooking spray.

Eggs, yogurt, maple syrup, vanilla, leavening agents in glass bowl.

Mix the liquid ingredients: In a large bowl, combine all the muffin ingredients except for the almond flour and blueberries, including eggs, maple syrup, yogurt, vanilla extract, citrus zest (if using), leavening agents, and salt.

Whisk well until there are no lumps.

Almond flour batter in bowl with red spatula.

Fold in almond flour: Scoop and measure almond flour, then level with knife to avoid overpacking which results in dense muffins. Gently fold into muffin batter with spatula.

Blueberries dusted with almond flour being stirred into muffin batter in a bowl.

Add the blueberries: First, combine the blueberries with 1 tablespoon of almond flour in a bowl and toss to coat them well. This is meant to help prevent them from sinking to the bottom of the batter.

Then add the blueberries to the batter and carefully fold them into the mixture with a spatula.

Unbaked blueberry muffin batter in liners placed into a blue muffin tin.

Bake the muffins: Use an ice cream scoop to divide the muffin batter between the 12 muffin liners.

Then bake the almond blueberry muffins in the oven on the middle rack for around 20 minutes.

Or until a toothpick inserted in the center comes out mostly clean. With a few crumbs is fine, but not “wet”.

Almond flour blueberry muffins in blue muffin tin.

Cool: Remove them from the oven and allow them to cool for at least 15 minutes before enjoying with some healthy iced coffee!

Tips and FAQs

  • Avoid dry sugar: The wet sweetener is needed for correct batter consistency, so I don’t recommend trying to use a granulated sweetener instead. Make these blueberry crumble bars if all you have is cane sugar.
  • Use liners: I highly recommend using lightly greased parchment paper muffin liners. I sprayed mine with cooking spray. That’s because almond flour muffins tend to stick even to the most well sprayed (even silicone) muffin tray.

Substitutions and Additions

  • Other berries: It’s possible to use a combination of berries or swap out the blueberries entirely for another berry like raspberry, cranberry, strawberry (chopped), etc. You may also love this healthy french toast casserole or healthy trifle both with fresh berries!
  • Yogurt: You can use plain regular (not Greek) yogurt, however might have to add 1/4 cup extra almond flour since it contains more liquid (whey). You can also use flavored yogurt. The goal is to bring batter to consistency in the photos, thicker than for pancakes.
  • Top with a citrus glaze: Like I do in healthy lemon poppy seed muffins!

Is Almond Flour Healthy?

Baking with almond flour results in baked goods that are very nutrient dense and packed with healthful fats and unrefined sugars. However, it is still fat and sugar, so like anything, it should be eaten in moderation.

Luckily, unlike many commercial muffins which are often described as “empty calories with the white flour and sugar and fat”, these muffins are a healthy breakfast idea.

They are packed with energy boosting nutrients and calories, which should help keep you full for longer. So, I actually think they’re great for those watching their weight.

You may also love this healthier almond flour chocolate cake!

Can I Make These Vegan?

I haven’t tried to veganize these muffins, though I have had luck by learning how to make a chia seed egg for almond flour banana bread. Then also, use a dairy free yogurt (Greek style, if possible).

However, I can’t guarantee results.

Can I Use Almond Meal or Other Flour?

If you’re wanting to use regular all-purpose flour, whole wheat flour, or spelt flour, even coconut flour, the answer is no. Make these healthy blueberry banana muffins, healthy lemon blueberry muffins, or try healthy blueberry bread instead with whole grains!

This recipe was designed with almond flour in mind, just like with my almond flour carrot cake.

If you can’t find any in store, you may be able to make some at home by blending blanched almonds in 10-second bursts into a floury consistency. I recommend sieving it and re blending to get the finest results.

I have not tried with almond meal, but in my experience baked goods with almond meal result in muffins with a dense texture.

Are these muffins keto?

While almond flour is keto friendly, I haven’t specifically designed this recipe to be low carb or keto, for example, as it contains maple syrup.

Why are my muffins with almond flour flat?

Usually, this is because you’ve ended up using a coarser almond meal rather than superfine almond flour.

Otherwise, leavening agents (baking powder and baking soda) that are no longer fresh are the main culprit of any flat baked good.

Can I make mini muffins?

All you need to do is reduce the baking time for mini muffins. I recommend checking on them at 10 minutes and baking until an inserted toothpick comes out clean.

A bite taken out of almond flour blueberry muffin showing texture and sitting on top of another muffin.

How Long Do These Muffins Last?

Store at room temperature between 2-3 days or in the refrigerator for up to 5 days, loosely covered rather than in an airtight container. As they’re moist, letting them “breathe” slightly is recommended.

To freeze, place cooled muffins in an airtight container with parchment paper between the layers of muffins and freeze for up to three months. When you want one, you can allow it to thaw in the fridge overnight or warm up from frozen.

More Almond Flour Recipes to Try

You might also enjoy this list of favorite almond flour recipes!

Healthy almond flour blueberry muffins on a counter, some stacked, with fresh blueberries.
Three healthy almond flour blueberry muffins stacked on top of each other.

Almond Flour Blueberry Muffins

Almond Flour Blueberry Muffins are tender, fluffy and naturally gluten free! They are perfect for a grab and go breakfast or snack.
5 from 15 votes
Servings 12 muffins
Calories 247
Prep Time 10 minutes
Cook Time 20 minutes
Total Time 30 minutes



  • Preheat oven to 350 degrees F. Line 12 muffin tin with parchment paper muffin liners (highly recommended) and spray with cooking spray. Set aside.
  • In a large bowl, add eggs, maple syrup, yogurt, vanilla extract, baking powder, baking soda and salt. Whisk very well until combined and no lumps.
  • Add almond flour (make sure to level the top with a knife and do not pack) and stir gently with spatula until well mixed.
  • In a small bowl, combine blueberries with 1 tbsp of almond flour and stir to coat evenly (this prevents them from sinking).
  • Add blueberries to the bowl with batter and give a few gentle stirs just enough to combine.
  • Using an ice cream scoop, divide batter between 12 openings of previously prepared muffin tin. Bake for 20 minutes on the middle rack or until toothpick inserted in the center comes out clean.
  • Remove from the oven, let cool for 15 minutes and enjoy.



  • Don’t substitute flour or liquid sweetener: Almond meal might work, muffins will be more dense and rise less. If you use dry sweetener, batter consistency will be offset. 
  • Frozen blueberries: No need to thaw.
  • Regular and other yogurt: You can use plain regular (not Greek) yogurt, however might have to add 1/4 cup extra almond flour since it contains more liquid (whey). Can also use flavored yogurt.
  • Use liners: Almond flour is delicate and muffins to tend to stick even to the most well sprayed and even silicone cavities.
  • Make Ahead: You can prepare the batter, minus the leavening agents and blueberries, up to a day in advance. Leave it covered in the refrigerator and mix in the baking powder + soda and coated blueberries before baking the muffins.
  • Storing: Store muffins at room temperature for 2-3 days or within the refrigerator for 5 days. As they’re quite moist, I’ve found they store better when loosely covered rather than in an airtight container.
  • Freezing: Freeze in layers with parchment paper between, in a large freezer bag. They will store in the freezer for up to three months.


Serving: 1muffin | Calories: 247kcal | Carbohydrates: 20g | Protein: 9g | Fat: 17g | Saturated Fat: 1g | Trans Fat: 1g | Cholesterol: 41mg | Sodium: 193mg | Fiber: 4g | Sugar: 14g
Course: Muffins and Quick Breads
Cuisine: North American
Author: Olena Osipov
Did you make this recipe?Mention @ifoodreal or tag #ifoodreal!

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About Olena

Welcome! I grew up in Ukraine watching my grandma cook with simple ingredients. I have spent the last 11 years making it my mission to help you cook quick and easy meals for your family!

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  1. 5 stars
    So delicious! Thank you for these recipes and the accompanying videos! I keep returning to this one for the blueberry muffins, because when we make them, they disappear from our kitchen too quickly! 🙂

  2. 5 stars
    Olena. You have the BEST BEST healthy recipes! Love love them 💕 I always go to you for something new! Keep them coming! Thanks Lisa 😁👍

  3. 5 stars
    Very moist and delicious! Thank you for this recipe. I wanted a little less sweetness, so I used 1/3 cup maple syrup and 1/2 cup plain low-fat yogurt. I had seen another recipe where beaten egg whites were folded in at the end of the recipe, so I used just the egg yolks in the first step and then folded in egg whites at the end. They turned out fantastic!

  4. 5 stars
    Good recipe but I think I under cooked them a little. I had them in for 19 minutes. Tops were brown and the toothpick came out clean so I was afraid to over bake them. They were very very very moist but the flavor was terrific. First time I made so next time I think I’ll leave them in a little longer and see what happens. Thanks

    1. Glad you enjoyed them! All ovens can vary, so noting what needs to be adjusted for yours is always a good idea! Enjoy!

  5. 5 stars
    Delicious…..Just made these with lemon zest had to add some almond milk batter was a bit thick even though I spoon measured my almond flour to not pack in..also baked 25min I have cancer so monk fruit / erythritol substitute for maple syrup 1/8 cup.. was perfect…..sugar feeds tumors

  6. 5 stars
    Love the muffins – nice flavor and moist! Since I don’t really like to use a lot of maple syrup, I blended a banana with a splash of oat milk and added some maple syrup to get to 1/2 cup. I also added lemon zest from one lemon – this added a really yummy flavor!

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