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These paleo blueberry muffins are out of this world! They’re perfectly sweet and tender, and you’d never think they were gluten and grain free. Made with honey, they’re spiked with just the right amount of lemon zest to give them that bakery taste. Refined sugar free, too, so no guilt here!

A stack of three paleo blueberry muffins with bite out of one

Deep breaths.

I. Am. A. Champion.

Freddie Mercury told me so. But really? It took me six rounds to get these muffins just right. And, if you read my blog or follow me on Instagram with any sort of regularity, you’ll know that I’m a bit of a perfectionist. So that means six rounds. In three days.

My poor dishwasher/husband.

But now? Lucky dishwasher/husband! They’re perfect. I didn’t want to settle for anything less than that and, by golly, you don’t have to, either.

What Makes This Recipe So Good

These blueberry muffins are:

  • Soft and tender but still firm. Not overly moist, not too soft.
  • Sweetened with honey and spiked with lemon zest.
  • Bakery-style with nice domed tops and a crunchy crust of cane sugar.
  • Really easy to make! You can make them in about 30 minutes, then they’ll cool for a few minutes after that.
  • Grain-free, gluten-free, dairy-free, and refined-sugar-free, if you skip the cane sugar topping.
  • Light and golden in color and in taste, thanks to the honey.
A paleo blueberry muffin in front of other muffins and a bowl of blueberries

Chef’s Tips

  • To use frozen blueberries, first rinse the blueberries in running, cold water until the water running off turns from a dark blue or purple color to a lighter blue or red color. Then dry the blueberries very, very well. Fold into the batter very gently.
  • Use parchment paper muffin liners for the easiest peeling ever. Or try a silicone muffin tin to pop out the muffins easily.
  • Fill the muffin tin almost to the very top. Use a 2-oz. disher to do this super quickly and easily.
  • Sprinkle the tops of the muffins with a very generous helping of cane sugar for a gorgeous, crackly topping. You want the tops totally and heavily coated for best results. You can skip this part and opt for a crumb coating, if desired. Try this recipe’s crumb top.

Frequently Asked Questions

How long do these last?

They’re best kept in an airtight container, but the tops will become a bit moister, rather than crackly from the cane sugar crust. However, they will stay good up to 5-6 days in an airtight container kept at room temperature.

They should freeze well, too.

Nut Free or Egg Free

These paleo blueberry muffins have not been tested with a nut-free or egg-free alternative. Both the almond flour and eggs are critical components of this recipe, so I cannot guarantee the result with either modification. If you’re looking for an alternative, try:

Can I skip the lemon zest?

You can! However, it doesn’t make them too “lemony,” just perfectly complemented, fresh, and springy!

Can I reduce the amount of honey?

You can, most likely. I would not reduce it below 3/4 cup without altering the rest of the recipe in some way, likely just reducing the amount of coconut flour and tapioca starch by 1 tablespoon each. I have not tested the recipe with these modifications (Since they’re essentially limitless!), but that should work!

Can I replace the honey with [granulated sweetener]?

No! I tested five batches of paleo blueberry muffins with granulated sweetener, and I didn’t get the perfect muffin until I used honey. More importantly, this recipe and the flours used are developed specifically to support a liquid sweetener. It’s possible that using maple sugar or erythritol may work, but I can’t guarantee anything.

Paleo blueberry muffin with a bite out of it in front of other muffins

Other Recipes You’ll Love

Recipe By: Cheryl Malik
4.34 from 3 votes

Paleo Blueberry Muffins

Prep 10 minutes
Cook 25 minutes
Cooling Time 10 minutes
Total 35 minutes
Light and fluffy blueberry muffins that are out of this world… and just happen to be paleo. Made with honey and lemon zest, they’re bakery quality with a nice dome and lovely texture.
11 muffins


Dry Ingredients

  • 2 cups blanched almond flour
  • ½ cup tapioca flour
  • ½ cup coconut flour
  • 1 cup honey
  • ½ teaspoon baking soda
  • ½ teaspoon salt

Wet ingredients

  • 2 eggs
  • cup almond milk
  • ¼ cup refined coconut oil melted
  • 1 tablespoon fresh lemon juice
  • 2 teaspoons vanilla extract
  • 1 ½ teaspoons lemon zest


  • 1 cups fresh blueberries
  • cane sugar for topping, optional


  • Preheat oven to 325º F and line a muffin tin with paper or parchment liners.
  • In a large bowl, whisk together all dry ingredients. In a medium bowl, whisk together all wet ingredients, except blueberries, until well combined. Fold wet ingredients into dry and stir until well combined. Fold in blueberries gently.
  • Portion the batter into prepared muffin tin, filling almost to the top of the liners.
  • Sprinkle with a generous amount of cane sugar for a topping then bake 25 minutes or until a toothpick inserted into the center comes out clean. Let cool 10 minutes in muffin tin then remove and let fully cool on a wire rack.
Note 1
To use frozen blueberries, follow these steps:
  • Rinse the blueberries in cold water until the water turns from blue to a very light red or blue. 
  • After rinsing, dry the blueberries very well with paper towels. 
  • Fold the blueberries into the batter quickly and gently; don’t overmix.
Note 2
These paleo blueberry muffins are best within a couple days of baking. Keep in an airtight container for best results, though they will become softer and moister after a couple days, due to the environment in the container. These should freeze well.
Note 3
You’re absolutely free to skip the sprinkle of cane sugar, or you can try maple syrup. Consider a paleo crumb top, like this recipe.
Note 4
I like parchment liners as they are totally foolproof and will not stick to any muffins!
Note 5
This recipe has not been tested with any other flour combination or sweetener. If you choose to use a powdered sweetener, like coconut sugar or erythritol, you might want to increase the milk just a bit. However, I cannot guarantee the results of any modifications to this recipe.
Note 6
To test for doneness, insert a toothpick into the center of a muffin. The toothpick should come out clean. After about 20 minutes of baking, test every 5 minutes.

Approximate Information for One Serving

Calories: 315calProtein: 6gFat: 16gSaturated Fat: 6gCholesterol: 29mgSodium: 189mgPotassium: 37mgTotal Carbs: 39gFiber: 4gSugar: 27gNet Carbs: 35gVitamin A: 50IUVitamin C: 2.3mgCalcium: 58mgIron: 1.3mg
Nutrition Disclaimers
Number of total servings shown is approximate. Actual number of servings will depend on your preferred portion sizes.
Nutritional values shown are general guidelines and reflect information for 1 serving using the ingredients listed, not including any optional ingredients. Actual macros may vary slightly depending on specific brands and types of ingredients used.
To determine the weight of one serving, prepare the recipe as instructed. Weigh the finished recipe, then divide the weight of the finished recipe (not including the weight of the container the food is in) by the desired number of servings. Result will be the weight of one serving.

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  1. I was also confused by the honey listed as a dry ingredient. I assumed that was a typo so I just added with wet ingredients. I also used only 1/2 cup honey bc 1 cup just seemed too much. I ended up doing mini muffins so I baked for 15 min instead of 25. They came out great! Love the lemon in them too!4 stars

  2. Were we supposed to mix in the honey with the dry ingredients? I thought this was a typo in the recipe so I mixed in the honey with the wet ingredients. Also, my batter was thinner looking than yours, yet I followed the recipe exactly. This resulted in having to bake them for 42 minutes, and the muffins fell in the in the middle. They tasted good, but were almost too sweet. I’d go with less honey next time?4 stars

  3. These look delish! For fresh blueberries, don’t you have to toss them in flour first so then they don’t sink to the bottom?

  4. Definitely do use the advised liners. I tried skipping that step and even with meticulous greasing I ended up digging out my muffins. Still very delicious, but also very ugly and had to eat them with a fork.

  5. I was almost out of honey so I used 1/2 cup and then added a dash of coconut sugar. Used coconut sugar on the top as well. Loved these!!5 stars

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