Healthy Chocolate Zucchini Muffins

When you have zucchini to use up, these chocolate zucchini muffins should be the first thing on your to-make list. They taste like a rich brownie (not a “healthy” one) and are naturally gluten-free and dairy-free.

I recently retested these muffins to see if I could improve them. Whenever I do this, I inevitably end up making at least 3 batches, because I’ll start to wonder things like, “Would baking powder make these rise better?” or “What if I added an extra egg or milk to the batter?”

As it turns out, I could make them a little better, so I’m glad I tried!

My kids are thrilled about having so many chocolate muffins in the house to taste-test, and I’m thrilled that we have after-school snacks that they are actually excited to eat. Each muffin has 6 grams of protein and 3 grams of fiber, so it will also help keep you feeling full and satisfied.

⭐⭐⭐⭐⭐ Featured Review

“My daughters and I love these muffins. I make them several times when zucchini is in season. They really do taste like brownies!”

-Katie

Chocolate Zucchini Muffin Ingredients

• Almond Butter. This is the magical ingredient that acts as a substitute for both flour and oil. Since it has so much fiber, you don’t need any grains! I do recommend shopping for “raw” almond butter (I like the one from Trader Joe’s), or use cashew butter instead, for a mild flavor that doesn’t compete with the chocolate.
• Zucchini. This adds moisture to the muffins, but you’ll hardly notice they’re inside! I do like to squeeze out the moisture before adding them to the batter to prevent the muffins from sinking in the center. If you don’t have a zucchini on hand, try my chocolate pumpkin muffins for a variation.
• Eggs. These give the muffins structure and add protein. I don’t recommend using an egg substitute here, because I don’t think the muffins will set in the center without them… but do be sure to check the comments, because some people have tried it!
• Cacao Powder. I always keep raw cacao powder in my pantry, so this is what I use in recipes. However, I think regular cocoa powder will work, too.
• Coconut Sugar. I love using granulated sugar in these muffins, and this is my go-to natural option. However, if you prefer to use maple syrup, check the comments below as some people have tried that, too.
• Chocolate Chips. If you want a double chocolate muffin (which makes them more brownie-like) stir in some mini chocolate chips! I like Enjoy Life brand to keep these dairy-free.

How to Make Healthy Chocolate Zucchini Muffins

Step 1:

Preheat the oven to 350ºF and line a muffin pan with 12 parchment paper liners.

Shred 1 medium zucchini using the largest holes of your box grater. (No need to peel it first.) I usually get 1 heaping cup of shredded zucchini from one that weighs about 6 to 7 ounces. Place the zucchini in the center of a thin dishtowel or cheesecloth, then gather the towel so you can squeeze-out the excess moisture. Set this aside while you prepare the muffin batter.

In a large bowl, combine 1 cup of raw almond butter, 3/4 cup of coconut sugar, 2 large eggs, 1/4 cup of cacao powder, 2 teaspoons of baking powder, 1 teaspoon of vanilla extract, 1/4 teaspoon of salt, and a 1/4 cup of milk or water.

Step 2:

Add the shredded zucchini to the bowl of muffin batter and fold in the chocolate chips. I like to reserve a few of the chocolate chips for topping the muffins later.

Then use a 1/4 cup measure (or a muffin scoop) to divide the batter evenly among the 12 muffin cups. Sprinkle a few chocolate chips on top, if you’d like to.

Bake these muffins at 350ºF for 25 to 30 minutes. You’ll know the muffins are done when your kitchen smells like brownies and the center of the muffins feels firm to a light touch. They should look dry on top.

Note: If you’re using a metal muffin pan, these will likely be done in the shorter time. I’m using a ceramic muffin pan in these photos (because I find it easier to clean) and it takes closer to 30 minutes to bake muffins.

Serving & Storage Tips

Let the muffins cool in the pan for at least 30 minutes. They are fragile while they are still warm from the oven, but will firm up as they cool. Once they are fully cooled, you can peel the wrapper away and enjoy!

Storage Tip: Leftover muffins can be stored in an airtight container in the refrigerator for up to 5 days, or in the freezer for up to 3 months. 

Recipe Variations I Tested

I recently tested this recipe 3 different ways to see if I could make it consistently more successful, as some readers had reported the muffins sinking in the middle after baking. I tested using baking powder instead of baking soda, and also experimented with adding an extra egg and some milk to make the batter easier to work with.

Below, you can see how the muffins compare. The winner (in my opinion) is the third one with the added milk and only 2 eggs. But the middle one made with 3 eggs is also great, so feel free try it that way as well.

Note: If you want to use baking soda instead of baking powder, as you can see, the muffins are more likely to sink in the middle.

Chocolate Zucchini Muffins (No Flour or Oil!)

4.99 from 102 votes

These chocolate zucchini muffins are almost too good to be true. They're made with zero flour or oil, yet they taste like a brownie. (Really!) You can hardly tell that there's zucchini inside. My kids usually inhale these too quickly to notice. You can stir the gluten-free batter together in about 10 minutes, so they are ready to bake in no time!

prep15 mins cook25 mins total40 mins

Servings:12 muffins

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Ingredients

 

US CustomaryMetric

 

1x2x3x

• 1 medium zucchini , shredded
• 1 cup raw almond butter
• ¾ cup coconut sugar
• ¼ cup cacao powder
• 2 large eggs
• 2 teaspoons baking powder
• ¼ teaspoon fine sea salt
• 1 teaspoon vanilla extract
• ¼ cup milk of choice
• ⅓ cup mini chocolate chips

Instructions

• Preheat the oven to 350ºF and line a standard muffin tin with 12 parchment cupcake liners. Place the shredded zucchini into the center of a thin dish towel, and squeeze out as much moisture as possible. Set this aside.
• In a large bowl, and add the almond butter, coconut sugar, cacao powder, eggs, baking soda, salt, vanilla, and milk. Stir well until the batter looks thick and glossy. Then stir in the shredded zucchini.
• Fold in the chocolate chips, if using, and then use a 1/4 cup to scoop the batter into the 12 muffin cups. Top with a few extra chocolate chips, if desired.
• Bake at 350ºF until the muffins have risen and feel firm to a light touch in the center, about 25 minutes to 30 minutes. (Your kitchen should smell like brownies when they are done!)
Note: The type of muffin pan you use will affect the baking time. My metal pan usually cooks muffins in 25 minutes, while a ceramic pan might require 30 minutes for the muffins to fully cook.
• Remove the pan from the oven and let the muffins cool for at least 20 minutes before serving. You can serve them warm or cold, but I think they have the best flavor when they are at room temperature. Leftovers can be stored in an airtight container in the fridge for up to 5 days, or in the freezer for up to 3 months.

Video

Notes

Nutrition information is for 1 of 12 muffins, without the optional chocolate chips. This information is automatically calculated and is just an estimate, not a guarantee.

Update Note: This recipe was updated in June 2026 to use baking powder instead of baking soda, and I also experimented with adding a 1/4 cup of milk to the batter. The resulting mixture fills the muffin tin better and prevents the muffins from sinking as they cool. 

Adding an Egg: I recently tested these muffins with 3 eggs instead of two. The resulting muffins are much sturdier this way, but a little less brownie-like. If you want to try this, don’t add the milk this recipe calls for and use 1 more egg instead. (So 3 eggs total.) 

Nutrition

Calories: 209kcal | Carbohydrates: 18g | Protein: 6g | Fat: 14g | Saturated Fat: 2g | Polyunsaturated Fat: 3g | Monounsaturated Fat: 7g | Trans Fat: 0.01g | Cholesterol: 32mg | Sodium: 87mg | Potassium: 310mg | Fiber: 3g | Sugar: 11g | Vitamin A: 98IU | Vitamin C: 3mg | Calcium: 122mg | Iron: 1mg

Author: Megan Gilmore

Course: Dessert

Cuisine: American

Keyword: chocolate zucchini muffins

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More Zucchini Recipes to Try

• Zucchini Oatmeal
• Zucchini Smoothie
• Vegan Chocolate Cheesecake
• Zucchini Lasagna
• Zucchini Pesto

If you try these gluten-free chocolate zucchini muffins, please leave a comment and star rating below letting me know how you like them.