Paleo Blueberry Muffins

4.95 from 19 votes
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Paleo blueberry muffins are a protein-packed baked good made with grain-free and natural ingredients. Each tender muffin is bursting with blueberries for a satisfying, healthy breakfast.

Paleo blueberry muffins stacked up on a plate

Paleo blueberry muffins fresh from the oven are a delicious morning treat, bursting with antioxidant-packed blueberries and grain-free ingredients. The blend of three flours; almond, coconut, and arrowroot, provides a light texture with golden brown domed tops.

A generous amount of eggs are whisked together to provide air and structure to these baked goods. Each muffin is naturally sweetened with coconut sugar to add tenderness to each bite. The combination of ingredients provides a texture similar to whole-wheat flour, without the gluten. This is a great recipe for a Paleo diet snack.

Ingredients for paleo muffins on a table

How to Make Paleo Muffins

Is your pantry packed with paleo-friendly ingredients to do some serious baking? I have some essential components I always have on hand as gluten-free and grain-free substitutes for flour, dairy, refined sugar, and corn-free leavening agents. These paleo muffins require a few unique ingredients to help mimic the function of gluten found in all-purpose flour.

Nut and Starch Flour

Coconut, arrowroot, and almond flour work harmoniously together to create a muffin structure base that creates crisp muffin tops and fluffy centers. Using only one flour will not work as each provides its unique quality to the muffins, and balancing the amounts is the key.

Spatula mixing blueberries into the muffin batter


Coconut sugar is allowed in the Paleo diet because it’s a natural sweetener from the coconut blossoms of the coconut tree that’s made into a syrup and then dried. The trace amount of nutrients like iron, calcium, zinc, potassium and prebiotic fiber from inulin makes it a better substitute for granulated sugar. The bonus is the dried sugar granules provide similar functions in baked goods. It has a hint of molasses and earthy flavor.

Coconut Oil

It can be a substitute for butter in baking due to its high smoke point and neutral flavor unless you have some ghee available. It comes in refined or unrefined options. The coarse product has more of a coconut flavor.

Muffin tin filled with blueberries and batter before being baked

Leavening Agents

Baking soda and cream of tartar are often used in combination with Paleo baking. Baking powder contains corn starch to keep it from caking together over time, which is not allowed on the Paleo diet.


Fresh blueberries are then folded into the muffin batter just before baking. I love how the juicy dark berries pop and create a jammy flavor in the muffins. I like to add a few extra on the top so that they form a prettier surface with more fruit baked in. A little bit of coconut sugar is sprinkled on top to add a little crunchy sugar glaze.

Muffin tin filled with paleo blueberry muffins fresh from the oven

High rise, golden brown paleo blueberry muffins are a beautiful pastry to be devoured by all. Because coconut flour contains fiber, I find the texture to be similar to whole-wheat muffins, but not as grainy or dry as it can sometimes be. The muffin tops add a slight crunch while the blueberries keep the bread moist and flavorful.

These paleo muffins are perfect for meal prep. Make a batch, eat a few fresh and then wrap the extras in plastic wrap and freeze. Grab and reheat anytime you need a quick bite! The moisture from the blueberries causes the muffins to get soggy after about a day if you don’t enjoy them right away, so it’s best to eat them the same day or freeze for later. I hope you enjoy!

Paleo blueberry muffins on a wire cooling rack

More Paleo recipes

Incorporating arrowroot flour

Arrowroot has become a trendy ingredient to use in paleo and gluten-free baking. The starch is flavorless and acts as a binder of water, creating a light and soft texture in muffins. After mixing with the liquid ingredients, the batter should sit for 30 minutes. This gives the starch time to absorb the water and gives a less gritty texture in the pastry.

Paleo Blueberry Muffins

Paleo blueberry muffins are a protein packed baked good made with grain-free and natural ingredients. Each tender muffin is bursting with ripe blueberries for a satisfying paleo diet breakfast.
4.95 from 19 votes
Prep Time40 minutes
Cook Time25 minutes
Total Time1 hour 5 minutes
Servings 12 servings
Course Breakfast
Cuisine American


  • 1 cup arrowroot flour
  • 3 large eggs
  • ½ cup water
  • ¼ cup coconut oil, divided, melted and cooled
  • 1 tablespoon pure vanilla extract
  • 1 teaspoon kosher salt
  • 1 tablespoon lemon juice
  • cup coconut sugar
  • 3 cups almond flour
  • 3 tablespoons coconut flour
  • 1 ½ teaspoons baking soda
  • ¼ teaspoon cream of tartar
  • ½ teaspoon cinnamon
  • teaspoon nutmeg
  • 2 cups blueberries


  • Adjust oven rack to middle position and heat to 325°F (163°C).
  • Melt 1 tablespoon of coconut oil. Use a brush to oil the insides of a 12 cup muffin pan with the coconut oil. Set aside.
  • Using a stand mixer fitted with a whisk, combine on medium speed arrowroot flour, eggs, water, 3 tablespoons melted coconut oil, vanilla, lemon juice and coconut sugar, 1 minute.
  • Allow mixture to rest for 30 minutes in the bowl. Meanwhile, prepare the rest of the batter.
  • In a medium-sized mixing bowl whisk together the dry ingredients; almond flour, coconut flour, baking soda, cream of tartar, cinnamon and nutmeg.
  • With the mixer set to low speed, add the flour mixture to the wet ingredients and mix until incorporated, 30 seconds.
  • Scrape the bowl and increase speed to high, whip batter until light and fluffy, 1 minute.
  • Fold in 1 ½ cups of the blueberries.
  • Divide batter evenly among a muffin tin, fill to the top.
  • Use the remaining ½ cup of blueberries, evenly distribute and place on top of the muffins.
  • Sprinkle coconut sugar on the tops of the muffins.
  • Bake until golden brown and a toothpick inserted in the center comes out clean, about 25 minutes, rotating halfway through baking.
  • Allow muffins to cool in the tin for 10 minutes.
  • Carefully remove and transfer to a cooling rack to cool before serving.


  • Recipe adapted from America's Test Kitchen, Paleo Perfected
  • Arrowroot flour is also called arrowroot powder or arrowroot starch.
  • Bob's Red Mill superfine almond flour was used.
  • Muffins are best enjoyed that same day. They can be stored in an airtight container at room temperature for up to 1 day. Warm in the oven at 300°F (149°F) for 10 minutes.
  • Muffins can be individually wrapped and stored in a resealable bag in the freezer for up to 3 weeks. Microwave for about 1 minute and then warm in the oven at 300°F (149°F) for 10 minutes.
  • Frozen blueberries can be substituted for fresh blueberries. Defrost and rinse with water, and then dry on paper towels to absorb excess moisture.

Nutrition Facts

Serves: 12 servings
Calories 280kcal (14%)Carbohydrates 27g (9%)Protein 7g (14%)Fat 18g (28%)Saturated Fat 5g (25%)Polyunsaturated Fat 3gMonounsaturated Fat 8gCholesterol 44mg (15%)Sodium 394mg (16%)Potassium 103mg (3%)Fiber 4g (16%)Sugar 13g (14%)Vitamin A 100IU (2%)Vitamin C 4.1mg (5%)Calcium 50mg (5%)Iron 1.3mg (7%)

Percent Daily Values are based on a 2000-calorie diet. All nutritional information is based on estimated third-party calculations. Each recipe and nutritional value will vary depending on the brands you use, measuring methods, and portion sizes per household.

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Jessica Gavin

I'm a culinary school graduate, cookbook author, and a mom who loves croissants! My passion is creating recipes and sharing the science behind cooking to help you gain confidence in the kitchen.

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  1. Laurene says

    I made these muffins last weekend and eaten them throughout the week. They have kept up great in the fridge and 30-40 sec in microwave makes them almost as good as fresh out of the oven. I highly recommend these muffins!!

    • Jessica Gavin says

      Thank you, Laurene! I love reheating the muffins too, it’s like they just came out of the oven! I also freeze them and reheat them.

  2. Kent says

    Eager to try these! Working on recipes for awesome daughter in law with major issues. I live at 9200′ elevation in Colorado. Would it be wise to raise the oven temp a bit and cook longer? Would also like to tweak this for a ‘dinner roll.’ Would using more arrowroot and less almond flour make it lighter. I am happy to experiment, just prefer a better/eatable outcome!
    thank you!

    • Jessica Gavin says

      For high elevation baking it is recommended to increase the temperature 15 to 25 degrees to help the proteins in the batter set faster since there is more pressure. Try 350 degrees F and see if that works. Check for doneness at 15 minutes, and keep monitoring every few minutes since it will bake faster at higher temperature. You might also need to let in sit in the tin for 15 or so minutes if the outside is cooked but the center still needs a little time. If it also rises too fast and falls, try reducing the baking soda to 1/2 teaspoon. Please let me know how it goes!



    Just made these and they taste good but the center is too moist (toothpic came out clean)

    Any idea how to prevent that or if I can better this batch?

    Thank you,


    • Jessica Gavin says

      Hi Diane- Did it seem like you could bake for a few minutes longer without the sides getting too brown? I would increase the time a few minutes, or let it cool in the pan for 15 minutes instead of 10.

  4. Esther says

    Letting the arrowroot soak for 30 minutes is a new concept to me, but that makes total sense!! I am looking forward to trying them.
    I just have one question, my husband can’t have coconut so I was wondering if I could omit it and perhaps up the amount of almond flour to compensate. Do you have any idea how much I would need to replace the coconut flour? I was thinking maybe 9 tablespoons extra almond flour instead of the 3 tablespoons of coconut flour.

    • Jessica Gavin says

      Hi Esther- I would first try replacing the coconut flour with 3 tablespoons of almond flour. If the batter seems too wet, then you can reduce some of the water, as coconut flour soaks up a lot of moisture. Try the first option, then if that’s not a hit, we can chat more about water amounts.