Decadent, rich, and made without a hint of flour or refined sugar, these paleo double chocolate zucchini muffins are also moist, fluffy, and super fast to make. An easy one-bowl muffin recipe, they’re ready within just 30 minutes!

Top down view of a wooden cutting board with double chocolate paleo zucchini muffins on top, with a striped napkin on the side.

This post was originally published with the title “One-Bowl Flourless Double Chocolate Zucchini Muffins”, we’ve changed the name and updated it to improve the post but it’s the same great recipe!

About this Recipe

We grow a few veggies & herbs at home, and inevitably our garden starts sprouting more leftover zucchini than we know what to do with.

So we’ve been zoodling, grilling & roasting them, and, of course, making LOTS of this amazing chocolate chip zucchini bread.

But I also wanted to create an easy muffin recipe for quick, grab-and-go breakfasts & snacks too (because let’s be honest…doubling down on chocolate is never a bad idea).

And that’s how these rich, decadent and veggie-loaded paleo zucchini muffins, with easy-to-find ingredients and minimal prep steps, came to be!

The combination of the almond flour and cocoa powder helps create a tender, fluffy crumb while keeping this one-bowl muffin recipe totally flourless.

While the ingredients are all wholesome, refined sugar free and healthy enough to eat for breakfast, the chocolate batter studded with ooey gooey chocolate chips makes these taste like a total treat! 

These double chocolate paleo zucchini muffins have been so popular around here I’ve been making double batches and freezing half for later in the week. They can actually go directly from the freezer into a lunch box and will defrost by lunch (love that!).

Top down view of a wooden cutting board with double chocolate paleo zucchini muffins on top, with a striped napkin on the side.

Process & Tips

I’m a big believer that gluten-free and paleo recipes don’t have to be overly complicated to be totally & completely delicious!

In the spirit of keeping-it-simple, all the ingredients can be mixed together in one bowl to keep the clean up (and dirty dishes) to a minimum.

You can use a cookie scoop (or a large tablespoon) to scoop the batter into a greased muffin tin, and then they’re off to bake for 15-20 minutes.

Really, the hardest part about this double chocolate paleo zucchini muffin recipe is just waiting for them to cool before tearing them open & taking that first bite.

Got lots of leftover zucchini too? I like to grate it, store it and stash it away in the back corner of the freezer. If you pre-measure it into the perfect zucchini bread-making (or zucchini muffin-making) amounts, then you’ll be ready for baking even in the cold months.

What Makes These Paleo Muffins Rise?

These muffins rely on baking soda for rise, along with a little extra help from the eggs!

Close up of a cutting board with chocolate muffins stacked on top of it and chocolate chips sprinkled around.

Best Types of Flour for Gluten Free Muffins

There are so many gluten free flour mixes and options on the market, but to keep this recipe easy and accessible (even if you don’t have a specialty store nearby) we use almond flour or oat flour. 

Almond flour is my choice for paleo friendly quick breads & muffins, but oat flour is great nut-free and gluten-free option too. 

You can use these two flours interchangeably in many of my recipes.

How to Make Double Chocolate Paleo Zucchini Bread

This muffin batter can also be used to make zucchini bread! 

Simply pour the batter into a greased 9×5 inch loaf pan and bake for 40-45 minutes (or until the edges begin to pull away from the sides and a toothpick comes out clean). 

Allow to cool in the pan for 5 minutes, then cool the rest of the way on a cooling rack prior to slicing and enjoy!

Top down view of a wooden cutting board with double chocolate paleo zucchini muffins on top, with a striped napkin on the side.

Ingredients & Modifications

Grated zucchini: Zucchini is the signature ingredient in these muffins and helps keep them extra tender, moist and filling. If you’re using these as a hidden-veggie muffin, you can peel the zucchini before grating to help the vegetable blend in. Otherwise no need to peel beforehand!

Almond flour: Finely ground almond flour works best for these zucchini muffins and is my go-to choice for paleo baking recipes. For a nut-free option, you can substitute oat flour in place for almond flour.

Cocoa powder: The unsweetened cocoa powder helps keep this flourless recipe extra rich, decadent and provides the extra chocolatey flavor to the batter.

Dark chocolate chips: The dark chocolate chips are what make this a double chocolate zucchini muffin! They bring that ooey gooey chocolate texture and flavor that makes them extra good. For a paleo and dairy-free option, be sure to look for dairy-free chocolate chips. I’ve linked my favorite for you in the recipe card below.

Coconut oil: I used melted coconut oil in this recipe. You can substitute any neutral flavored oil in its place, such as avocado or canola.

Eggs: I haven’t tested this as a vegan recipe with flax eggs or vegan egg replacer. If you try it, be sure to let us know how it turns out!

Unsweetened applesauce: The applesauce adds subtle sweetness and helps keep these muffins tender and moist.

Pure maple syrup: I like the flavor of maple syrup in this recipe but you can also use honey as an alternative refined sugar free sweetener. You can add a bit more maple syrup if you prefer a sweeter muffin.

Vanilla extract: Vanilla extract always pairs well with chocolate baked goods and really helps to play up the dessert-like flavors in this muffin.

Baking soda: Together, with the eggs, the baking soda helps these gluten free muffins rise.

Kosher salt: Look for kosher salt with the regular iodized salt at the grocery store (it has a subtler flavor). Use less iodized salt if that’s what you have on hand.

Tip: look for individual serve unsweetened applesauce cups for this recipe. Each cup is typically ⅓ cup, the exact amount you need for this recipe without any wasted or leftover.

How to Store & Freeze Leftover Muffins 

Keep in a tightly sealed container at room temperature for 48 hours. Or store in the fridge for up to 3-4 days.

Past 4 days you’ll want to freeze any leftover muffins. I like to store mine in a sealed ziptop bag or freezer friendly container for up to 2-3 months.

If you live in a high humidity environment, I recommend refrigerating your paleo zucchini muffins after baking.

Top down view of a wooden cutting board with double chocolate paleo zucchini muffins on top, with a striped napkin on the side.
5 stars (4 ratings)

Double Chocolate Paleo Zucchini Muffins

These double chocolate paleo zucchini muffins are moist, fluffy, and so satisfying. This easy one bowl muffin recipe is decadent, rich and made without a hint of flour or refined sugar. (And the best part? They’re ready within 30 minutes!).


  • ¼ cup melted coconut oil, plus more for greasing the pan
  • 2 large eggs
  • cup unsweetened applesauce
  • cup pure maple syrup
  • 2 teaspoons vanilla extract
  • 1 ½ cup finely ground almond flour
  • cup cocoa powder
  • ½ teaspoon baking soda
  • ¼ teaspoon kosher salt
  • 1 cup loosely packed grated zucchini
  • cup dark chocolate chips, plus more for topping*


  • Heat the oven to 350F.
  • In a large bowl, whisk together the coconut oil, eggs, applesauce, maple syrup, and vanilla extract.
  • Add the almond flour, cocoa powder, baking soda, and salt. Stir gently until just incorporated. Add the zucchini and stir again until just combined.
  • Add in the chocolate chips and stir to combine.
  • Fill each section of a 12-section muffin tin with roughly ¼ cup batter, then bake for 15-20 minutes, or until the edges begin to pull away from the sides and a toothpick comes out clean.
  • Allow to cool in the pan for 5 minutes, then cool the rest on a cooling rack.


*Most chocolate chips include dairy. Be sure to use dairy-free if that’s important to you. I linked my favorite option for you in the ingredients list above.
Nutrition information calculated using almond flour.
For a nut-free version that’s still gluten-free, you can substitute oat flour in place of almond flour.
For more ingredients & modifications, see the full blog post above.

Nutrition Information:

Calories: 238kcal, Carbohydrates: 15g, Protein: 9g, Fat: 17g, Saturated Fat: 7g, Polyunsaturated Fat: 1g, Monounsaturated Fat: 2g, Trans Fat: 1g, Cholesterol: 151mg, Sodium: 159mg, Potassium: 177mg, Fiber: 3g, Sugar: 9g, Vitamin A: 242IU, Vitamin C: 2mg, Calcium: 82mg, Iron: 2mg
Nutrition disclaimer
Did you make this recipe?If you do, be sure to share it on Instagram and tag me at @realfoodwholelife so I can see!

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