Double chocolate zucchini muffins made grain-free, refined sugar-free, and dairy-free. These paleo healthy gluten-free zucchini muffins are perfectly sweet, fluffy, and moist.

Paleo Double Chocolate Zucchini Muffins - grain-free, refined sugar-free, dairy-free zucchini muffins for a healthy breakfast or snack | #glutenfree #recipe

Oh hey, zucchini season!

I have to admit, I eat an exorbitant amount of zucchini. I put it in Zucchini Herb Sausage Breakfast Casserole, Vegan Red Curry Zucchini Noodle Bowls, my Instant Pot Chicken Soup with Rice and so, so much more.

The sweet application of zucchini has always been a favorite of mine, too. I’m obsessed with these Paleo Chocolate Chip Zucchini Muffins and Paleo Double Chocolate Zucchini Bread, BUT NOW, these double chocolate zucchini muffins are really whetting my whistle.

Case in point: zucchini, zucchini, zucchini.

Grain-Free Chocolate Muffins with Zucchini - paleo, refined sugar-free, dairy-free zucchini muffins for a healthy breakfast or snack | #glutenfree #recipe

One of my favorite parts about this recipe, aside from the fact that it yields super rich muffins is that they don’t turn out overly sweet.

I like my muffins to be muffin-like rather than to taste like cupcakes. If you like a sweeter muffin, do feel free to add some coconut sugar or a zero-sugar sweetener like stevia, xylitol or erythritol.

How to Make Paleo Double Chocolate Zucchini Muffins:

There are a couple of ways you can make the batter for these muffins.

Option 1: Mix together the wet ingredients in a mixing bowl, and stir together the dry ingredients in a separate mixing bowl. Combine forces by pouring the wet into the dry and stirring well. Fill up the muffin tray with the batter, bake, and enjoy.

Option 2: Toss all ingredients except for the zucchini and chocolate chips into a blender. Blend until smooth. Fold in the chocolate chips and zucchini, then fill up your muffin cups and bake.

Regardless of the approach you take to preparing the batter, may I recommend that you sprinkle with coarse sea salt? I love the chocolate-salt combo, as I feel it really enhances the flavor and palatability!

Chocolate Paleo Zucchini Muffins - grain-free, refined sugar-free, dairy-free zucchini muffins for a healthy breakfast or snack | #glutenfree #recipe

Recipe Adaptations:

  • For cakier muffins, add 2 Tbsp avocado oil or coconut oil.
  • Add 3 Tbsp Coconut sugar or a couple drops of liquid stevia to make these muffins sweeter.
  • I use stevia sweetened chocolate chips to keep these muffins lower on the glycemic index, but you can use any chocolate chip or chunk you like.
  • Replace the almond flour with hazelnut flour.

Grian-Free Chocolate Zucchini Muffins - paleo, refined sugar-free, dairy-free zucchini muffins for a healthy breakfast or snack | #glutenfree #recipe

Zucchini muffins all around!

My cookbook, Paleo Power Bowls, is now available! CLICK HERE to check it out. Thank you for your support!

If you make these Paleo Chocolate Zucchini Muffins, please feel free to share a photo and tag @The.Roasted.Root on Instagram!

Paleo Double Chocolate Zucchini Muffins - grain-free, refined sugar-free, dairy-free zucchini muffins for a healthy breakfast or snack | #glutenfree #recipe

Paleo Double Chocolate Zucchini Muffins

5 from 2 votes
Grain-Free paleo double chocolate zucchini muffins are a cleaner muffin for breakfast or snack.
Prep Time 15 minutes
Cook Time 20 minutes
Total Time 35 minutes
Servings: 9 muffins



  • Preheat the oven to 350 degrees F. Line a muffin tray with muffin papers.
  • Whisk the eggs, pure maple syrup, and zucchini together in a mixing bowl (wet ingredients).
  • In a separate bowl, stir together the remaining dry ingredients.
  • Pour the wet mixture into the mixing bowl with the dry mixture and stir well until well-combined.
  • Pour muffin batter into the muffin tray, filling the holes 3/4 of the way up. Bake on the center rack of the oven 18 to 22 minutes, or until muffins are cooked through.
  • Remove from oven. Allow muffins to cool at least 30 minutes before peeling and eating.


Serving: 1of 9 · Calories: 318kcal · Carbohydrates: 32g · Protein: 8g · Fat: 20g · Fiber: 3g · Sugar: 19g
Author: Julia
Course: Breakfast
Cuisine: American
Keyword: almond flour, chocolate, gluten free, grain free, zucchini
Did You Make This Recipe?I want to see it! Tag @the.roasted.root on social media!
Paleo Double Chocolate Zucchini Muffins made with almond flour and pure maple syrup - a healthy and delicious treat! |

Julia Mueller
Meet the Author

Julia Mueller

Julia Mueller is a recipe developer, cookbook author, and founder of The Roasted Root. She has authored three bestselling cookbooks, – Paleo Power Powers, Delicious Probiotic Drinks, and The Quintessential Kale Cookbook. Her recipes have been featured in several national publications such as BuzzFeed, Self, Tasty, Country Living,, etc.

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Questions and Reviews

  1. Had a large zucchini to use up so made a double batch of these today–they’re awesome! Great texture on the inside and the muffin top is ever so slightly crisp, which I love. Added vanilla extract and the coconut oil variation, but no extra sugar. Subbed chopped pecans for chocolate chips (just a personal preference ?) Still sprinkled some chocolate chips on top, though! Already bookmarked in my favorites because I will absolutely be making these again. Thanks for sharing!

  2. What if I wanted to use bobs 1:1 flour? Would that be ok for the recipe? how much would I use instead of the tapioca and almond flour?

    1. Hi Rebecca,

      I’ve never tested the recipe using Bob’s 1:1, but I would replace the almond flour AND tapioca flour with 1.5 cups of BRM to start. If the batter seems too runny, I would add 1/4 cup more and see where that lands me 😉 Let me know how it turns out and how much flour you use! xoxo

  3. I was pleasantly surprised with this muffin recipe. I made it with my grand-daughter as her mom is gluten free. I had a little trouble knowing if they were done , so might have over-baked a bit, but, they were delicious. Think I would add 2T. avocado oil. Thanks for this great recipe.

    1. Thanks so much for sharing, Marleen! I’m happy you and your granddaughter enjoyed the recipe. The next time I make it, I’ll try it with 2 Tbsp of avocado oil and see how it turns out. Couldn’t be bad to add some additional moisture, right? 😉