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These Chocolate Chip Paleo Zucchini Muffins are fluffy, moist, and packed with good-for-you ingredients. Made with a combination of almond flour and coconut flour, this gluten-free muffin recipe is made with unrefined sweeteners, zucchini, dark chocolate and is the perfect grab-and-go breakfast!

Gluten free zucchini muffins with chocolate chips broken openChocolate Chip Paleo Zucchini Muffins

This Paleo Zucchini Muffin recipe is an OG Lexi’s Clean Kitchen and still a goodie all these years later! This recipe was originally published in celebration of LCK turning 1 back in 2014. We’re republishing today because this recipe has stood the test of time and is worth the photo facelift it got to reshare today!

These gluten free muffins made with a blend of almond flour and coconut flour have the perfect texture! They are the best way to use up zucchini and your picky eaters will never know there are some veggies inside the muffin! Grab one when you are running out the door, or for a guilt-free mid-day snack. They freeze well, too!

Chocolate paleo zucchini muffins in a tinIngredients for these Gluten Free Zucchini Muffins:

  • Almond Flour
  • Coconut Flour
  • Eggs
  • Honey
  • Vanilla
  • Unsweetened Apple Sauce
  • Baking PowderZ
  • Zucchini
  • Chocolate Chips

bowl of batter of almond flour zucchini muffinsIs Almond Flour Healthy?

I love using almond flour as the base for my muffin recipes because they make the best gluten-free muffins without needing to add a lot of other fussy ingredients. Almond flour is a delicious and nutrient dense alternative to any other flour. It is low in carbs and high in fat which makes it a great healthy flour that makes you feel fuller, longer.

How to Measure Almond Flour

If you have an electronic kitchen scale at home, it’s best to use it here to measure almond flour. Almond flour can be tricky to measure as it can be easily compacted, even straight from the bag. The same goes for coconut flour because such a small difference in measuring can impact a recipe because it’s such an absorbent flour. So we’ve included the weight in grams here. Any electronic kitchen scale can switch between grams and ounces, and grams are more precise so we’re offering that. If you don’t have a scale: lightly scoop the almond flour or coconut flour into the cup measurement and level it off.

Gluten free zucchini chocolate chip muffinsLooking for other recipes to use up zucchini? Check out these others:

If you like this muffin recipe, check out these:

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Chocolate Chip Zucchini Muffins

4.84 from 6 votes
These Chocolate Chip Paleo Zucchini Muffins are fluffy, moist, and packed with good-for-you ingredients. Made with a combination of almond flour and coconut flour, this gluten-free muffin recipe is made with unrefined sweeteners, zucchini, dark chocolate and is the perfect grab-and-go breakfast!
Servings 9
Prep Time 10 minutes
Cook Time 20 minutes
Total Time 30 minutes


  • 2 eggs
  • 1/4 cup honey
  • 1 teaspoon vanilla extract
  • 1/4 cup unsweetened apple sauce
  • 2 cups 192 grams almond flour
  • 1 tablespoon 7 grams coconut flour
  • 1/4 teaspoon fine sea salt
  • 2 teaspoons baking powder
  • 1/2 cup grated zucchini or 1/2 medium zucchini
  • 1/2 cup chocolate chips


  • Preheat oven to 350ºF and line a muffin tin with parchment paper liners.
  • In a mixing bowl whisk together eggs, honey, vanilla, and applesauce. Add in almond flour, coconut flour, salt and baking powder to combine.
  • Fold in grated zucchini and dark chocolate.
  • Fill muffin liners with a heaping 1/4 cup of batter and bake for 20 minutes.


This post was originally published in May 2014, and updated and republished in August 2019 with new photographs.


Calories: 125kcalCarbohydrates: 16.4gProtein: 3.4gFat: 5.9gSaturated Fat: 1.7gCholesterol: 36mgSodium: 69mgFiber: 1.6gSugar: 12g
Course: Breakfast, Snack
Cuisine: Gluten-free, Paleo
Author: Lexi

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Recipe Rating


  1. 5 stars
    Loved these! Came together so quickly and the applesauce tastes great with the chocolate. I added some peanut butter powder and vanilla protein as I’m trying to up my protein intake but am craving sweets so this was a perfect balance.

  2. 5 stars
    These muffins are INCREDIBLE! You would never know they aren’t made with wheat flour, they are the best muffin I’ve, in fact, ever eaten and how marvelous that Lexi created it so that I can make it at home! Delish!

    1. You can. Almond flour muffins tend to be a bit moist after freezing, but they’ll still taste good. Enjoy!

    1. Yes you can sub maple syrup. No, do not squeeze out the moisture. Typically if a recipe requires that, it will instruct it. At least, on this site!

  3. These muffins are absolutely delicious. Made several batches and I wouldn’t change a thing about this recipe.

  4. 4 stars
    Hi Lexi,

    I made these last night and my family loved them! Is there a way to get the nutritional info? It would load that information when I checked under the recipe page.

    1. The nutrition info is there: Calories 125 Calories from fat 45 Total Fat 5.9g Saturated Fat 1.7g Cholesterol 36mg Sodium 69mg Carbohydrate 16.4g Dietary Fiber 1.6g Sugars 12g Protein 3.4g

  5. Do you have to squeeze the moisture out of the zuchinni? And if I grease the muffin pan super well, do you think I can forego the liners?

  6. These were good but a little bland. Didn’t stop me from eating them all! haha – I might have added too much zucchini or not shredded it fine enough. I would make again and maybe add a little dash of cinnamon or something to help liven up the flavor a bit.

  7. Hey Lexi!

    Was wondering if I could make this recipe into a ‘bread’ instead of muffins if you thought that would work?

    1. That would change the recipe. You can likely sub more almond flour for the coconut flour and with some adjustments, remove the tapioca. See older muffin recipes on my page, those don’t include tapioca.

  8. These muffins look so delicious! We usually have some friends give us zucchini during the summer; this recipe will be on the must-make list! 🙂

  9. Yum! I want to try them! What chocolate chips did you use? Thanks! and Greetings from Germany 😉

  10. Happy one year blog anniversary!! I am a big fan of your recipes and always enjoy reading your blog. These muffins look amazing! I can’t believe there’s zucchini in them!

  11. You should be SO proud! I’m honoured to have been a part of even a tiny piece of your journey. Congrats gorgeous! Can’t wait to see what the future and your new house will bring!!!

  12. Yay to your new home!! Such exciting times! Your recipe looks super yummy and a great recipe to start off the 2nd year of your blog! 🙂

  13. Congrats on your new home and your anniversary, both so great! These are amazing by the way, one of my favs. Have a great week!