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
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257 comments on “Paleo Blueberry Muffins”

  1. I found your site about 5 mos ago. Every recipe I have made has been great! My husband started having health issues & his food choices were very restrictive. I made this blueberry muffin recipe except made it into a loaf. He ate most of the loaf & he has never been a fan of paleo foods. Am making it, again, this morning for a visit with an old friend. Thank you so much!!5 stars

  2. So delicious! My son and husband loved them! Thank you for the recipe. 5 stars

  3. My husband is allergic to almonds, is they a substitute for it I can use in the blueberry muffins recipe?

  4. Thanks Lisa! This is my second time making these, and they turned out great :) I added lemon juice and zest as well.5 stars

  5. Hi Lisa,

    As always, thank you for your fantastic recipes and all you do! Question for you. Do you think it would be okay to swap out the ACV for lemon juice?5 stars

  6. Hi Lisa,

    Is the nutrition content that you provided for 1 muffin. I have to watch my carbs and sugars so I want to make sure 1 muffin is equal to 26 grams of carbs and 16 grams of sugar. I was searching for the serving size but didn’t see it listed under the nutrition content. I have PCOS and try to treat it naturally through diet and exercise. I appreciate your gluten-free, dairy-free, and low sugar options!

    Thanks for your recipes and for all you do. I love watching your videos on YouTube! Congrats on your new cook book as well!

  7. Baked these today and they turned out delicious. Loved them 💕

  8. If I already have a paleo mix with all the above flours in one, do I just add a little less than 3 cups of the paleo mix?

  9. Wow…my whole family loved these!! They couldn’t even tell that they were paleo or “healthy”. Such an amazing recipe and will definitely make again!!5 stars

  10. They look sooo yummy. Though, mine ended too wet and the dough didn’t rise well…any idea on what to improve? hint, i used a partly de-oiled almond flour and i used european baking poweder instead of baking soda (i doubled the amount).

    • I would try to stick with the original ingredients as much as possible. The baking soda should help the bread rise!

  11. Yuuuuum!! I added cinnamon and lemon zest and they are super yummy! The tops browned quickly but taste good anyways. Bookmarking this recipe for sure! Thank you!!4 stars

    • Thank you so much for this clean and healthy recipe, Lisa! I Made this recipe twice and loved the taste both times! This is my go-to, guilt-free dessert/breakfast! When I made it the second time it turned out a little bit wet even though I already increased the time in the oven. Do you know where I could have gone wrong?5 stars


  13. Wondering if the this blueberry muffin recipe could sub flax eggs for real eggs? Same for the Zucchini muffin recipe (for egg allergy).  

    • I haven’t tried this with a flax egg, but it might work. If you try it, let me know how it turned out!

  14. These are the best paleo muffins I’ve ever made! I used honey cause I didn’t maple syrup, added a little cinnamon and they were delicious! My kids loved them too. 5 stars

  15. I just baked these and they are cooling now. I can’t wait to try them! What is the serving size for the nutrition facts? Thank you! 

  16. My whole family loved these! You would never know they are paleo and are just the right amount of sweet.5 stars

  17. Another grand slam muffin recipe! I made these blueberry muffins, & they were fantastic! And I’m usually not a big fan of blueberry muffins, but my husband & I really enjoyed them. Thanks again for sharing your delicious, healthy recipes! I would love for you to share a carrot cake or pumpkin muffin recipe.5 stars

  18. This has changed all my perspectives about blueberries, I am gonna try this recipe and I think this will be the best in taste to start the morning.
    Thanks!5 stars

  19. Is there any substitution for the tapioca flour? I have all the other ingredients on hand….lol

  20. Exactly what I was looking for. These are delicious!5 stars

  21. Hands down best paleo muffins I’ve ever made. The flavor was delicious and the tops got a nice crunch! My kids loved them. There will definitely be a staple in my home. I subbed grass fed butter for the coconut oil no problem!5 stars

  22. If I wanted to make lemon blueberry muffins, would it work to sub lemon juice for the cider vinegar in this recipe? Or would that be lemony enough?

  23. If I were to make this non dairy free would I replace the coconut oil with butter?

    • Yes, you can use butter in replacement of coconut oil.

    • These were incredible! Moist, not overly sweet, fruity!

      I was in the mood for a lemon blueberry muffin so I replaced the ACV with lemon juice and added some lemon zest to achieve the flavour. Turned out great!

      Thanks for sharing Lisa!5 stars

  24. Thanks you Lisa! These were delish! I used 1/4 cup of maple syrup and 2 tablespoons of golden monk fruit sweetener, added 2 extra tablespoons of water and swapped almond milk for coconut. 
    I also used frozen blueberries in half and 1/2 diced Granny Smith apple with cinnamon in the other half and both are great. Do you think I can change and add poppyseed and lemon to a batch?5 stars

    • Glad you enjoyed these muffins! I actually am planning to do a potential lemon poppyseed version soon. So will keep you updated!

  25. My daughter says “I just want to eat these muffins all day”5 stars

  26. These are incredible, and they’re my go-to when I want something quick for breakfast throughout the week. The only issue is that they don’t make it that long – everyone loves them, and we eat a whole batch in about 24 hours! They’re super flavorful in the best way, and I think they even taste much better than your average gluten and refined sugar muffin. Also, the recipe is pretty quick to throw together! Highly recommend!!5 stars

  27. These were great! Plush and tasty.  I added a bit of lemon zest. Could easily imagine turning these into cranberry orange muffins, too.

    Would you please make a note in the recipe that the coconut oil should be melted? I had to search in the comments to confirm that. It might be obvious for those who bake a lot with coconut oil, but it’s an easy enough thing to mention for beginners.5 stars

  28. I made these earlier this week and hands down best paleo muffins I’ve ever made! The top was crispy when they came out of the oven, which I love, and they also taste good straight out of the fridge. Thank you!
    And I’m baking the banana ones for the first time right now.5 stars

    • Gotta love a soft inside and a crisp topping when it comes to muffins! Hope you enjoy the banana muffins as well :)

  29. My husband has recently been told to stop eating gluten and dairy. I was worried because he started eating a lot of gluten free cakes and biscuits. I know that gf items are high in starch and that’s not good for diabetes. By chance I stumbled on here and I love the recipes. These muffins are divine. Moist and fluffy. And my husband loves them too5 stars

    • Packaged GF items are not the best as they usually have lots of other additives, so homemade is the way to go! Happy to hear he’s loving these muffins and hopefully he can enjoy other baked Downshiftology goods :)

  30. Lisa I made these yesterday and they are so tasty , my hubby is asking for me to make weekly.  Just the right texture and sweetness, all your recipes I have tried as been a hit.  My picky son asked for your Splatchocked chicken for Sunday dinner tomorrow, so will be making that.  Thanks for all your delicious recipes. Blessings!5 stars