These healthy blueberry zucchini muffins are made with almond flour, naturally sweetened with maple sugar, and packed with juicy blueberries. Gluten free, paleo, dairy free, and perfect for breakfast or snacks.
These healthy blueberry zucchini muffins are one of my favorite ways to use summer zucchini!
They’re soft and tender with plenty of juicy blueberries, bright lemon flavor, and just enough sweetness from maple sugar. Made with almond flour and naturally gluten free, they’re perfect for breakfast, lunchboxes, afternoon snacks, or meal prep.
Even if you’re skeptical about zucchini in baked goods, you’ll never know it’s there beyond the incredible moisture it adds to every bite!
Why You’ll Love These Blueberry Zucchini Muffins
- Soft, moist texture without being heavy
- Packed with juicy blueberries
- Naturally gluten free and dairy free
- Paleo friendly and refined sugar free
- Great for meal prep and freezing
- A delicious way to use summer zucchini
Key Ingredients for the Best Zucchini Muffins
Blanched Almond Flour
Blanched almond flour keeps the muffins tender while adding healthy fats and protein. This recipe also uses tapioca flour (or arrowroot) and coconut flour to give the muffins the best structure while keeping them grain free and moist.
Zucchini
Finely shredded zucchini adds moisture without making the muffins taste like vegetables.
Blueberries
Fresh blueberries burst as they bake, creating pockets of juicy sweetness throughout the muffins. I like to use smaller blueberries to avoid the blueberries taking over the muffins and adding too much water.
Lemon
Fresh lemon juice and zest brighten the flavor and make the blueberries pop.
Baking soda and baking powder
To help the muffins rise
Refined coconut oil
Coconut oil gives the muffins moisture while keeping them dairy free. I like to use refined coconut oil for baking to avoid coconut flavor.
Eggs
Eggs give the muffins structure along with the flours, and also help them rise.
How to Make the Best Blueberry Zucchini Muffins
The biggest secret is squeezing as much moisture as possible from the zucchini before folding it into the batter. This helps create bakery-style muffins with a soft crumb rather than a gummy texture.
For the prettiest muffins, save a handful of blueberries to press onto the tops before baking.
Storage and Freezing
Store leftover muffins covered at room temperature for up to 2 days or refrigerate for up to 5 days.
To freeze, place cooled muffins in a freezer-safe bag or container and freeze for up to 3 months. Thaw overnight in the refrigerator or warm gently before serving.
Recipe Variations
- Use frozen blueberries without thawing.
- Add chopped pecans or walnuts for crunch.
- Replace the lemon zest with cinnamon for a cozier flavor.
- Sprinkle the tops with a little maple sugar before baking for a bakery-style finish.
FAQ
Do I need to peel the zucchini?
No. The peel is soft and adds color and nutrients to the muffins.
Can I use frozen blueberries?
Yes. Add them directly from frozen and gently fold them into the batter.
Why do I need to squeeze the zucchini?
Removing excess moisture helps prevent dense or gummy muffins and improves rise.
Can I freeze blueberry zucchini muffins?
Absolutely. These muffins freeze beautifully for up to 3 months.
Are these muffins paleo?
Yes. They’re made with almond flour, naturally sweetened with maple sugar, and are completely grain free and dairy free.
If you’re looking for a healthy muffin recipe that tastes like a treat, these Blueberry Zucchini Muffins deliver every time.
They’re packed with summer blueberries, naturally gluten free and paleo friendly, and perfect for making ahead for busy mornings and snacks throughout the week!
Once you try them, don’t be surprised if they become your favorite way to use up zucchini all summer long.
For More Paleo Muffin Recipes, try one of these!
*Recipe updated June 2026: The recipe has been simplified and improved with more blueberries, fresh lemon zest, and a lighter texture for even better flavor and bakery-style muffins.
Healthy Blueberry Zucchini Muffins (Gluten Free, Paleo, Almond Flour)
Ingredients
Wet Ingredients:
- 2 large eggs at room temperature
- 1/2 cup maple sugar
- 1/3 cup refined coconut oil melted and cooled slightly
- 1 teaspoon pure vanilla extract
- 1 tablespoon fresh lemon juice
- 1 teaspoon finely grated lemon zest
Dry Ingredients:
- 2 cups blanched almond flour
- 1/3 cup tapioca flour
- 2 tablespoons coconut flour
- 1 teaspoon baking soda
- 1 teaspoon baking powder
- 1/2 teaspoon fine sea salt
Mix-Ins:
- 2 cups finely shredded zucchini squeezed very well, about 2 med zucchini
- 1 cup fresh blueberries plus a few extra for topping
Instructions
-
Preheat your oven to 350°F. Line a 12-cup muffin pan with parchment liners.
-
In a large bowl, whisk together the eggs, maple sugar, coconut oil, vanilla, lemon juice, and lemon zest until smooth.
-
In a separate bowl, combine the almond flour, tapioca flour, coconut flour, baking soda, baking powder, and salt.
-
Stir the dry ingredients into the wet ingredients until just combined. The batter will be thick.
-
Gently fold in the squeezed zucchini until combined, then the blueberries, saving a handful to place on the top of the muffins.
-
Allow the batter to rest for 3 minutes so the coconut flour can absorb moisture.
-
Divide the batter evenly among the muffin cups, filling them nearly to the top. Press a few extra blueberries onto the tops of the muffins.
-
Bake for 23–25 minutes, or until the tops are golden and a toothpick inserted near the center comes out clean.
-
Cool in the pan for 10 minutes, then transfer to a wire rack to cool completely.
Nutrition
Note: This post contains Amazon affiliate links. This means that if you click on a link and make a purchase, I will receive a small commission at no cost to you. Thank you for supporting Paleo Running Momma!
I made these today and they were delicious my mom loved them! Can’t wait to try more recipes!
These are so good! I brought them to work, and they were a hit. Thank you for sharing!
Sounds great, glad you enjoyed!
I only have 1 med zucchini, could I grate some carrot to replace the missing zucchini?
UPDATE! I used a cup of carrot and a cup or zuke and it turned out perfectly. These are definitely worth writing into the recipe family cookbook!
Happy you liked them!
These are sooooo good! Making them for the third time today. So flavorful yet light tasting. A big hit with my husband too!
I replaced the tapioca flour with coconut flour and they were delicious.
Absolutely obsessed with this recipe, I made one batch and my two kids 18months and 3 years as well as my husband were gobbling them down so I made another batch!!! They are moist, sweat and delicious! Thank you for this and all of your amazing recipes!!!!
Just tried making these for the first time with my son. We love them and they aren’t sweet, but just enough to satify a craving for something unhealthy!
I’ve made these several times and they’re delicious! I’ve been doing 6 tablespoons of coconut sugar. Is that correct? The lower case “t” throws me off so I’m wondering if it’s supposed to be teaspoons.
I bake a lot GF/DF goods and these are the first muffins I’ve made that look and tastes like a normal muffin. They didn’t deflate and sink in when they cooled. I did substitute 1 cup of zucchini with 1 cup of carrots just to add a variety of veggies and they turned out great!
Sounds great!!
Just made it! Tastes great! Thank you!!!