Paleo Blueberry Muffins

Paleo blueberry muffins are a sweet and cozy way to start your morning. They’re moist, fluffy, and have a burst of fresh blueberries with every bite.

Three paleo blueberry muffins stacked on top of each other.

If you’ve made my all-time favorite paleo lemon blueberry cake before, this muffin recipe should look very familiar. It’s basically a simplified version of the cake — minus the lemon!

These gluten-free muffins are light, fluffy, perfectly sweet, and studded with fresh, juicy blueberries. Perfect as a healthy breakfast option or sweet afternoon snack!

Paleo blueberry muffins ingredients in bowls.

Paleo Blueberry Muffin Ingredients

  • Dry Ingredients: My gluten-free flour trio for baking is almost always almond flour, tapioca flour, and coconut flour. Then you’ll just need baking soda, kosher salt, and fresh blueberries.
  • Wet Ingredients: Nothing fancy here — eggs, milk, maple syrup, coconut oil, apple cider vinegar, and vanilla extract.

Find the printable recipe with measurements below.

Paleo blueberry muffins in a muffin pan.

How To Make Paleo Blueberry Muffins

Like many of my muffin, cake and quick bread recipes, you’ll mix the dry and wet ingredients separately then whisk them together. It ensures the muffins stay light and fluffy!

  • Make the batter. Mix the wet and dry ingredients separately. Then whisk in the wet to the try until a smooth batter is formed.
  • Fold the blueberries into the batter. I personally like to save some blueberries to top onto the muffins right before baking!
  • Bake the muffins. Pour the batter into each muffin cup until its 85 to 90% full. Then bake for 28 to 33 minutes at 350°F. Make sure to do the toothpick test to make sure the insides are cooked!
Paleo blueberry muffins on a cooling rack.

Tips For The Perfect Muffins

  • Don’t overmix the batter. You want to quickly blend the batter and immediately pour it into the muffin pan. That will help make the muffins nice and fluffy.
  • Fresh vs frozen blueberries. Fresh is ideal for this recipe. But if you only have a pack of frozen blueberries on hand, that works too. Just note that you do not need to thaw them prior, otherwise you’ll be left with soggy muffins. Just fold the frozen blueberries into the batter directly.
  • Freeze an extra batch. Because these are freezer friendly, it might be a good idea to keep a stash on hand. You never know when you can use them for a quick breakfast or snack on-the-go!
Paleo blueberry muffins cooling.

Storage Tips

Although these muffins taste the best the day they are baked, leftovers keep well at room temperature for about 3 days. After that, you can store them in the fridge for about one week.

And if you want to freeze them, just store in a freezer-safe container for up to 2 months. When you want to enjoy, you can thaw them in the fridge or on the counter. Once thawed, you can also warm them up in the microwave if you want to cut them in half and add a pat of butter.

One paleo blueberry muffin with wrapper peeled.

More Gluten-Free Baked Goods

In the mood to bake up a storm? Here’s some of my all time paleo bread and baking recipes to try this week.

If you make these paleo blueberry muffins, let me know how they turned out in a comment below!

Paleo blueberry muffins stacked on top of each other.

Paleo Blueberry Muffins (Healthy Blueberry Muffins)

4.96 from 85 votes
Prep Time: 10 mins
Cook Time: 30 mins
Total Time: 40 mins
Servings: 12 servings
Author: Lisa Bryan
Paleo blueberry muffins are sweet, moist and fluffy! They're also gluten-free and dairy-free. It's a healthy version of the classic recipe you know and love.


Dry Ingredients

  • 2 cups almond flour
  • 2/3 cup tapioca flour
  • 1/4 cup coconut flour
  • 1 teaspoon baking soda
  • 1/2 teaspoon salt
  • 1 1/2 cups blueberries

Wet Ingredients

  • 2 eggs, room temperature
  • 1/3 cup almond milk
  • 2/3 cup maple syrup
  • 1/4 cup coconut oil, melted
  • 1/2 tablespoon apple cider vinegar
  • 1 teaspoons vanilla extract


  • Preheat your oven to 350 degrees fahrenheit and line a muffin pan with baking cups.
  • Add all of the dry ingredients to a mixing bowl and whisk together.
  • Add all of the wet ingredients to a separate mixing bowl and whisk together. Then, add the wet ingredients into the dry and whisk for about 30 seconds, until you have a batter.
  • Fold the blueberries into the batter. You can always reserve a few blueberries to add to the top of the muffins before baking.
  • Evenly divide the batter between 12 baking cups. They should be about 85-90% full.
  • Bake the blueberry muffins for 28-33 minutes, or until they're lightly golden on the top and a toothpick comes out clean.

Lisa’s Tips

  • For all of the flour brands I use and recommend, make sure to check out my Shop page.


Calories: 249kcal, Carbohydrates: 26g, Protein: 5g, Fat: 15g, Saturated Fat: 5g, Cholesterol: 27mg, Sodium: 215mg, Potassium: 65mg, Fiber: 3g, Sugar: 13g, Vitamin A: 50IU, Vitamin C: 2mg, Calcium: 72mg, Iron: 1mg
Course: Breads
Cuisine: American
Keyword: Paleo Blueberry Muffin Recipe, Paleo Blueberry Muffins
©Downshiftology. Content and photographs are copyright protected. Sharing of this recipe is both encouraged and appreciated. Copying and/or pasting full recipes to any social media is strictly prohibited.
DID YOU MAKE THIS RECIPE?Leave a comment below and share a photo on Instagram. Tag @downshiftology and hashtag it #downshiftology.

Leave a Comment

All comments are moderated before appearing on the site. Thank you for sharing your feedback!

Recipe Rating

Your email address will not be published. Required fields are marked *

257 comments on “Paleo Blueberry Muffins”

  1. These are the best paleo muffins I’ve made. The perfect amount of sweet and not grainy at all. Delicious. 5 stars

  2. Hi Lisa! I love your recipes and have found lots of inspiration lately. However, I am allergic to almonds so I cannot have almond flour. Do you have any suggestions for a replacement, even if it is not paleo? I have been wanting to make so many recipes that require almond flour and I am feeling bummed that I can’t have any of them. Thank you!

  3. Hi!

    Love your recipes. Have recently had great success with the tuna salad (it really is the best!), falafel bread, baba ganoush and chicken salad. My children (3+5) love all of these recipes!

    Tried this one and though they were eaten up, I found them to be really soggy. I cooked for the recommended time and the tooth pick came out clean. I followed the recipe exactly! Any fixes for this? Should the coconut oil be solid or liquid when added?

    Thank you!5 stars

    • Hi Jessica – it sounds like they may just need a little more time in your oven, as all ovens cook slightly different. Also, make sure that if the blueberries were fresh and washed that they were completely dry. Hope that helps!

  4. Another winner! Made a few tweaks for ingredient preferences and flavor additions. I used arrowroot instead of tapioca and coconut milk instead of the almond milk, added 1t cinnamon & 1/4t almond extract, reduced the maple syrup to 1/2c, and subbed lemon juice for the acv & added 1T lemon zest. Next time I’ll probably use smaller wild blueberries, but these are so delicious! Can’t wait to share them! I keep finding more and more recipes of yours I want to make. Thanks again. 5 stars

  5. Great if you love coconut. Wonderful texture and taste- with or without blueberries. 5 stars

  6. I had all the flours in my pantry, so thought I would test these out. I only made half the recipe as a test… Everyone in the family LOVED them and now I have to make more! Our son helped with the baking. So easy and delicious!! I should have  known as I love all your recipes. Oh and we also made the chocolate chia pudding last night… can’t wait to try today 😀5 stars

  7. Hi Lisa- these muffins are delicious ! I didn’t have tapioca flour, so substituted it with all purpose flour. Don’t think these will last very long (especially under the lockdown and working from home)!!
    Thank you for the amazing recipe. 5 stars

  8. These muffins are so easy to make and they taste delicious. Thank you Lisa, all your recipes are easy to follow and they are a hit with my husband and 13yo son. 5 stars

  9. HI Lisa-

    These look delicious and I want to make them. I have been trying to use healthier flours, but my kids know and don’t love the taste. Compared to muffins with all-purpose or whole wheat pastry flour, do your blueberry muffins taste much different? Maybe I will make half this batch and see how it goes:). Thank you. Btw, I since home, have been making the aqua frescas and dijon salmon many times!

    • Hi Michelle- I always make sure my paleo baked goods taste just like the real thing, so I wouldn’t worry about that! Can’t wait to see how your family likes these :)

  10. These are fantastic- taste just like a regular blueberry muffin but so much healthier.
    I didn’t have tapioca flour on hand so used cassava flour instead.
    I was skeptical about freezing them but I just thawed out 2 a month later and they still taste amazing.5 stars

    • Hi Alex – So glad you enjoyed these muffins! And never worry about freezing these, as I always do and the texture and taste remains the same :)

  11. I can’t believe I waited so long to make these. They were certainly worth the wait! I thank you and my neighbors thank you! 5 stars

  12. Yet again, another great recipe Lisa! Fluffy texture of the cooked muffin! I used fresh blueberries and they didn’t sink to the bottom! This batter is sweet and delicious. Anyone who likes blueberries will love this recipe! These are my boyfriends favorite muffin now! I plan to bake some for our families! Thank you Lisa! Btw, I also made the same batter from this muffin recipe, however instead of blueberries, I put cooked apples at the bottom of the muffin tin! They are like apple upside down cakes! YUM! 5 stars

    • Hi Karen- Looks like you found another winning muffin recipe :) I love the idea of apples at the bottom too. I’ll definitely have to try that next time.

  13. Hi, is it possible to use all almond flour and leave the rest out? If I were to try this how would I compensate? Thanks!

    • Hi Patti – You can try using all almond flour, but it might come out a bit more dense than usual. Instead of tapioca flour, you can also use arrowroot flour or any gluten-free flour blend :)

  14. Another great recipe! I love these. They turned out just like a muffin should. We have been snacking on them throughout the week. Big hit with the kids, which is always a good thing.5 stars

  15. p.s. love your site. Thank you!!

  16. Hi Lisa,

    I’d love to make this (and many other recipes) but unfortunately am allergic to tree nuts. Is there any other flour that you’d recommend as a substitution for almond flour? I have coconut, tapioca, oat and brown rice flours.

    • Hi Kathy – unfortunately, I haven’t tried any of those flour substitutions and each flour bakes slightly different. So I’m not sure how they would turn out.

  17. Best muffins ever! I substituted blueberries for frozen mixed berries and it came out beautifully. I love how you add all those tips and tricks into the post to help us make substitutions with things we already have in the house. This is actually the first muffin my little baby daughter has ever tried and she loved it too. These will be a staple in our household now. Thank you!! Xx5 stars

    • Hi Alice – I love how you used mixed berries in this. And I feel honored that this is the first batch of muffins your daughter has tried :)

  18. These were seriously the best muffins ever, and the fact that they are paleo make them even better! My family finished an entire batch within 12 hours of making them. Thank you for this recipe Lisa, I can’t wait to make these again soon :).5 stars

  19. Looks amazing! Any advice on how I could make them lemon blueberry? Like the muffin version of your cake?

  20. These are the best blueberry muffins! Thank you, Lisa!5 stars

  21. Hi, what other substitutes would you recommend for the tapioca flour other than arrowroot or cornstarch? What about oat flour or white whole wheat flour? Thank you!

  22. Hi Lisa,

    I don’t have muffin cups, or pan. Can I bake it like a cake and use a porcelain baking dish? If so, I have two dish sizes, an 8 x 10, or a 9 x 13. Which size would you suggest? Also, would the bake time change?


    • Hi Barbara – I’m sure you could bake it in a baking dish. Unfortunately I don’t know the best size for this as I haven’t tried it. I’d recommend looking at some online baking calculators to see if you can find the equivalent size for a dozen muffins. Best of luck!

      • Lisa,

        I took a chance, and based on the amount of batter, I used an 8×10 baking dish, as well as substituted hazelnut flour (which is what I have on hand at the moment)  in place of almond flour. I baked the “cake” at your suggested time of 33 minutes and it turned out beautifully, cooked through and moist. Next time, if using hazelnut flour, I think I will add lemon zest to add a little zing.5 stars

      • Hi Barbara – I’m so glad your blueberry loaf turned out perfectly! Adding lemon next time will add some beautiful freshness to this.

  23. Thanks so much for such great recipe, I have made it twice. 5 stars

  24. These are so delicious and super easy to make!! I recommend doubling the batch – one to eat now and the other to freeze. Yum!5 stars

  25. Can you substitute canned coconut milk for the almond milk?

  26. I am so excited to try these but I am not able to use almond flour, do you have any suggestions for a flour I could substitute in its place?

  27. I really enjoy your healthy tips and recipes, Lisa! I’m allergic to tree nuts. Is there something I can substitute for almond flour in all your yummy looking Paleo baking recipes? Thanks for sharing all your knowledge and joy of health!

    Meg5 stars

    • Hi Meg – Thanks so much! I’m happy you love my recipes. For the almond flour, it’s hard as there aren’t 1:1 substitutions on individual GF flours. I’d recommend trying with a nut-free GF flour blend though. :)

  28. What can I substitute for almond flour? Cassava flour?
    Love your recipes!

  29. Hi Lisa! I just baked them and since it was my first time baking with frozen blueberries, I unfortunately had my batter turned into blue. Lesson learned to try fresh ones next time. . :( The taste though… 5 stars!!!!5 stars

  30. Will baking them directly in the muffin pan effect the consistency and/or baking time?

  31. These muffins are so good!  They are didn’t last long though. My family ate them all up!  I was hoping to have one for breakfast too. I already have requests to make them again. A new family favorite! Thank you Lisa for another delicious recipe.5 stars

    • Hi Jacquelyn- Oh no! Looks like you’ll have to whip up 2 batches next time :) Happy to hear you and your family loved these muffins.

  32. I just prepared these this morning while we are social distancing. I’m a weight trainer of 12 yrs and have been following a paleo meal plan for 1 year now. I typically do not eat any sweets but hey why not I have nothing but time now. I came across Lisa’s recipe and must say they are absolutely delicious. I followed the recipe exactly as Lisa’s posted it, my husband doesn’t eat sweets as well and he is not a guru of fitness or nutrition as I am. Long story short I froze them as recommended. Thank you Lisa for sharing I will definitely bake these again. Go to treat!5 stars

    • Hi Somer- It definitely doesn’t hurt to have sweets every now and then :) Plus, these make for a great freezer treat to save for a later day!

  33. Is there anything that can be substituted for almond flour?  I am sensitive to almonds.   Flax meal?

  34. I just made this recipe, instead of the almond milk I used lemon juice and zest, just like in the paleo lemon blueberry cake recipe, because I LOVE lemon🍋 and I can’t stop eating this, soooo delicious 😋 
    Thank you for all the amazing recipes ✨5 stars

  35. Hey there!! 

    Can I substitute the tapioca  flour? Here in Germany it’s quite hard to it on supermarkets :(

  36. I would love to know your recommendation for an almond flour replacement. I can sub the almond milk easily enough, but which flour would yield similar results? Coconut? Hazelnut? Even a gluten-free grain would be okay. Thanks!

    Also, if we omit vanilla (due to allergy) does it need to be replaced by something of similar consistency, or is it for flavor only?

    Lastly, I’m assuming the vinegar serves a specific purpose but I can’t have that either (or lemon juice!). Is there anything else that the vinegar could be substituted with? Thanks so much!

    • Hi Lina – you could sub hazelnut flour for the almond flour. The vanilla is for flavor only, and you could sub the vinegar with cream of tartar (it helps make them fluffy). Hope that helps!

  37. Made ’em this morning! 100% awesome! Didn’t have tapioca flour and replaced it with cornstarch (1/3 cup). They were fast and easy. Making a double batch next time. Thank you, Lisa!5 stars

    • Hi Kathy – Good to know this recipes comes together with cornstarch in replacement of tapioca flour!

    • Hi Lisa,

      I haven’t tried these yet but I do love all your recipes! I was wondering if the coconut flour makes these taste coconutty? And if so, is there any other flour you can substitute it for? 

      • Hi Kaila – You won’t taste the coconut flour in this recipe :) If you don’t have that, you can also try using arrowroot flour or any gluten-free flour blend.

  38. Yes! I can’t wait to try these already. Your photos are definitely the “eating with my eyes” kind.

  39. Yum! A breakfast with this Paleo blueberry muffins is heaven! I love blueberries so much and this recipe is no exception. I love that moist and fluffy texture. Delicious in every bite!5 stars

  40. This looks so good!   I can’t wait to try this.  

  41. All your recipes are amazing, and so healthy!
    Thanks Liza ❤️  5 stars

  42. Wonderful recipe to enjoy in Argentina. Take care 💕5 stars

  43. Looks really good! with what can I substitute the coconut flour? More tapioca flour would work? Thanks for your amazing blog and all that you share!

    • Coconut flour is quite different than any other flour as it’s highly absorbent. You could try with just more of the other flours, but it may impact the texture.

  44. The muffins turned out great. Loved how easy they were to make due to the tips and tricks for the blueberry muffins. I will be saving this recipe to make another time.5 stars

  45. Blueberry muffins are one of my faves. I’m definitely going to be making this soon.5 stars

  46. I love a good blueberry muffin. Yours look perfect.5 stars

  47. Blueberry muffins are my all-time favorite breakfast item. I’m excited to try a healthier version!5 stars

    • Hi Kelly – These are great breakfast option for a quick and easy sweet treat that’s also a bit on the healthier side :)

  48. Looks awesome, Lisa! Thank you so much, as always. May I ask you about servings – how many servings are in one batch. Just trying to understand the macros implications – is it just one muffin, I assume, and how many muffins do you get from the batch? Thank you!!!

  49. Have not made them yet but surely will. Can yiu substitute Tapioca flour? Thank you!

  50. Can I use monk fruit instead of maple?

    • Hi Gabby – I haven’t tried using monk fruit, but I’m sure it could work! You will have to play around with the quantity though.