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Pinch Me Good! » Breakfast » Double Chocolate Zucchini Muffins – Gluten Free

Double Chocolate Zucchini Muffins – Gluten Free

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Chocolate zucchini muffins are a healthy sweet breakfast treat! They are made with zucchini, almond flour and chocolate for a nice moist and fudgy muffin that even the kids will love!

Zucchini chocolate muffin on paper with more zucchini around it.

These Chocolate Zucchini Muffins were such a hit with my family. I was so excited!. I love that these gluten free muffins are healthier since we are sneaking some veggies into them but trust me they are still going to be so delicious!

Also, chocolate for breakfast is just the best, especially with a nice hot cup of coffee. And once it is zucchini season around August, you will have so much zucchini. This chocolate muffin recipe will come in handy.

I think shredded zucchini should be put in every baked dessert. It’s like this magic ingredient that is hidden in the most delicious sweet treats like in this Zucchini Banana Bread and Zucchini Cake and nobody can tell!

The best part is that there isn’t really much flavor to the zucchini either so nobody will even notice it is in there. What a great trick!

If you have never tried to add zucchini to baked goods then you MUST TRY this recipe! See tips for baking with zucchini below.

Double chocolate muffins with zucchini

Why you’ll love this chocolate zucchini muffin recipe

  • Super moist and fluffy!
  • Gluten free and refined sugar free!
  • Packed with healthy fat and nutrients
  • Super fudgy and decadent
  • Kid-friendly and mom-approved!
  • Double chocolate overload! Yum!

Ingredients needed for chocolate chip zucchini muffins

Ingredients for chocolate zucchini muffins in bowls with labels over each ingredient.
  • Zucchini – you will need about 1 medium zucchini, shredded with the water squeezed out of it.
  • Almond flour – you can also use coconut flour but it may alter the taste a bit.
  • Cocoa powder – dark chocolate cocoa powder is what I used for that deep chocolate color and flavor.
  • Non-dairy milk – any unsweetened non-dairy milk will work
  • Almond butter – creamy, not chunky
  • Egg – 1 large egg is all you need
  • Maple syrup – make sure it is real maple syrup or you can use honey
  • Applesauce – unsweetened
  • Chocolate chips – I used dark chocolate chips
  • Baking soda – make sure it is gluten free
  • Vanilla – pure vanilla extract adds a nice warm flavor to the muffins.
  • Salt – helps to balance all the sweet and savory notes.
  • Olive oil – extra virgin olive oil or you can also use coconut oil or melted butter.

How to make healthy chocolate zucchini muffins

Here is a summary of how to make these gluten free chocolate zucchini muffins with step by step photos to help guide you. Get the complete list of recipe ingredients, instructions and nutrition in the recipe card at the bottom of this post.

Shredded zucchini in a cloth with the water squeezed out.

Step 1: Shred the zucchini and place it into a towel and squeeze the extra moisture out of it.

Wet muffin ingredients mixed in a bowl.

Step 2: Combine the wet ingredients in a medium mixing bowl.

Step 3: Add in the shredded zucchini and chocolate chips.

Step 4: Mix to combine everything into a thick chocolatey batter.

Chocolate muffin batter divided between lined muffin cups in a muffin pan.

Step 5: Divide the muffin batter between the muffin cups in a lined muffin pan.

Baked double chocolate zucchini chocolate chip muffins in a silver muffin pan.

Step 6: Bake on the middle rack of a preheated oven until a toothpick inserted in the middle of one of the muffins comes out mostly clean.

How long to bake chocolate zucchini muffins

These gluten free muffins take about 25 minutes to bake but ovens do vary so you want to check them at around 22 minutes. Some Zucchini muffin recipes may take longer based on the recipe.

Baked chocolate muffins with zucchini in a muffin pan with one of the muffins on top of the pan.

Tips for baking with zucchini

Zucchini is so great in baked goods because it has a delicate, light flavor that blends so beautifully into batters and gives any sweet treat a nice moist and light consistency.

  • Shred it as fine as you can so that it blends well into the batter. I like to use a box grater to do this since it has a fine grate side to it. This allows it to basically disappear into any batter, which is why nobody will even know it is in there.
  • Read the recipe you are using because some recipes will call for you to squeeze the extra water out of the zucchini before adding it to the batter and some recipes will have you leave it as is. This is the science of baking, haha.

Note: In this chocolate zucchini muffins recipe, you will need to squeeze the water out of the zucchini since we add in some other wet ingredients.

Double chocolate chip muffin with a bite taken out of it.

FAQs

Do I need to squeeze the water out of the zucchini for this muffin recipe?

In this muffin recipe, you do have to squeeze the extra water out of the zucchini.

How do you store double chocolate zucchini muffins?

Once the zucchini muffins are fully cooked and cooled, you can transfer them to an airtight container and keep them on the counter or in the pantry for up to 3 days.

Can I freeze these muffins?

Yes, you can! Place the fully cooked and cooled muffins into a freezer-friendly container and keep them in the freezer for up to one month. Defrost in the refrigerator overnight and enjoy.

Expert tips for making gluten free chocolate zucchini muffins

  • Finley shred the zucchini and squeeze the extra water out by using a clean kitchen towel. This will make the zucchini the perfect texture in these chocolate zucchini muffins.
  • Mix up the batter well so that the zucchini is well distributed throughout the batter.
  • Don’t overfill the muffin cups with too much batter. Use an ice cream scoop to evenly distribute the batter between the muffin cup cavities.
  • Check the muffins at around 22 minutes of baking and insert a clean toothpick in the center of one of the muffins to see if they are done. If the toothpick comes out with some wet crumbs on it then they are done. If not, then let them bake for a few more minutes.
  • Let the muffins cool. These muffins need about 15-20 minutes to cool after baking. This will allow the muffin liners to easily pull away from the muffins and result in perfectly cooked fudgy chocolate zucchini muffins.

More healthy muffin recipes to try!

  • Gluten Free Cranberry Orange Muffins
  • Healthy Apple Muffins – Gluten Free
  • Sausage and Pepper Breakfast Egg Muffins
  • Gluten Free Chocolate Chip Muffins
  • Healthy Pumpkin Protein muffins
  • Best Healthy Zucchini Muffins

Did you try this recipe? If you did then please leave a rating and comment below. I would love to hear how yours turned out!

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Zucchini chocolate muffin on paper with more zucchini around it.

Chocolate Zucchini Muffins


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4.5 from 4 reviews

  • Author: Amy Estes
  • Total Time: 32 minutes
  • Yield: 12 muffins 1x
  • Diet: Gluten Free
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Description

These double chocolate zucchini muffins are perfectly fudge, chocolatey and decadent and are the best summer sweet treat. Nobody will believe they are actually healthy! Enjoy these muffins for breakfast or a snack anytime!


Ingredients

Scale
  • 1 + ¼ cup blanched almond flour
  • ⅓ cup cocoa powder – unsweetened 
  • 1 teaspoon baking soda
  • ½ teaspoon kosher salt 
  • 1 large egg – lightly whisked
  • ⅓ cup maple syrup
  • ¼ cup unsweetened applesauce
  • ¼ cup creamy almond butter
  • ¼ cup non-dairy milk – like almond or coconut milk
  • 1 tablespoon olive oil or coconut oil
  • 1 teaspoon vanilla extract
  • 1 cup shredded zucchini – with the extra water squeezed out
  • ⅔ cup chocolate chips – plus more for topping


Instructions

  1. Preheat the oven to 400° F and line a 12-cup muffin pan with muffin liners.  Set aside. 
  2. Prepare the zucchini: shred the zucchini using a box grater.  Place the shredded Zucchini into a clean kitchen towel and wring out the extra water from the zucchini. Set aside. 
  3. In a medium size mixing bowl, mix up the dry ingredients: almond flour, cocoa powder, baking soda and salt.
  4. In a separate mixing bowl mix up the wet ingredients: egg, maple syrup, applesauce, almond butter, milk, olive oil, vanilla extract.
  5. Combine the wet and dry ingredients and mix well then fold in the shredded zucchini and chocolate chips.
  6. Divide the batter evenly between 12 muffin cavities of a 12-cup lined muffin pan and bake at 400°F for 22-25 minutes, until a toothpick inserted in the center of one of the muffins comes out mostly clean. 
  7. Remove, let cool and enjoy these incredible chocolate zucchini muffins!

Notes

  • Finley shred the zucchini and squeeze the extra water out by using a clean kitchen towel. This will make the zucchini the perfect texture in these chocolate zucchini muffins.
  • Mix up the batter well so that the zucchini is well distributed throughout the batter.
  • Don’t over fill the muffin cups with too much batter. Use an ice cream scoop to evenly distribute the batter between the muffin cup cavities.
  • Check the muffins at around 22 minutes of baking and insert a clean toothpick in the center of one of the muffins to see if they are done. If the toothpick comes out with some wet crumbs on it then they are done. If not, then let them bake for a few more minutes.
  • Let the muffins cool. These muffins need about 15-20 minutes to cool after baking. This will allow the muffin liners to easily pull away from the muffins and result in perfectly cooked fudgy chocolate zucchini muffins.
  • Storage: You can store these muffins in a container on the counter for up to 3 days or freeze them in a freezer-friendly container for up to 1 month. Defrost overnight on the counter.
    • Prep Time: 10 minutes
    • Cook Time: 22 minutes
    • Category: Healthy Breakfast Ideas
    • Method: Baked
    • Cuisine: American

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    Filed Under: Breakfast, Favorite Summer Recipes, Gluten-Free, Kid-Friendly, Meal Prep, Oven

    Reader Interactions

    Comments

    1. Sheryl

      July 25, 2021 at 11:15 pm

      Can I use oat flour? I can’t have Almond flour

      Reply
      • Amy

        July 31, 2021 at 8:38 am

        Hi Sheryl, I have not tested this recipe using oat flour but I am pretty sure it would work in place of the almond flour. Just make sure it is ground up nice and fine.

        Reply
    2. Protima

      July 26, 2021 at 10:55 am

      Hi,

      Could I use something different in place of applesauce?
      Thanks

      Reply
      • Amy

        July 31, 2021 at 8:37 am

        Hi Protima, You could use canned pumpkin or plain Greek yogurt in place of the applesauce.

        Reply
    3. Chantal J

      August 7, 2021 at 2:26 pm

      Hi Amy, I tried this recipe twice. First time was with Dutch processed cocoa and they sank so I did it today with regular cocoa and they sank too. The taste was delicious though. Do you know why they would sink?

      Reply
    4. Erica

      August 13, 2021 at 8:42 pm

      Can you replace the almond butter with something else?

      Reply
      • Amy

        August 16, 2021 at 12:41 pm

        Hi Erica, you could use creamy peanut butter, cashew butter or sun butter in place of the almond butter. I will add this to the recipe notes. Thank you so much for asking.

        Reply
    5. Tara

      August 22, 2025 at 8:49 am

      So good! I thought I had applesauce, but I didn’t , so I used coconut oil there and A2 milk because that’s what I had. Otherwise I made as is. They were just right in sweetness once the chocolate chips were added. Perfect snack. I don’t use almond flour too often, so I wasn’t sure how I would like the texture, but I didn’t notice a difference, yet they were filling so I wasn’t as tempted to overeat.

      Reply
      • Amy Estes

        September 6, 2025 at 6:12 pm

        Hi Tara, I am so glad you enjoyed them!

        Reply
    6. Mallory

      November 9, 2025 at 3:27 am

      These are delicious, but mine all just fell apart! Like they are too fudgy/moist. I still have half of the batter left? Can I add more flour or maybe all purpose flour to try to keep them from falling apart on the next go round?

      Reply
      • Amy Estes

        November 13, 2025 at 10:48 am

        Hi Mallory, I am so sorry your muffins fell apart. I have made this recipe many times and have never had that happen. I would try allowing them to cool a bit longer since zucchini muffins tend to crumble if you cut them before they have fully cooled. Also make sure you are measuring your flour using a proper measuring method.

        Reply
    7. Audrey

      March 29, 2026 at 7:35 pm

      These are SO good! I did half oat flour and half almond flour and it worked great. Hoping to try it with a flax egg next so my mom can try some! Definitely wait 15 minutes for them to cool before eating so the wrapper doesn’t stick.

      Reply
      • Amy Estes

        April 8, 2026 at 3:12 pm

        Thank you Audrey! I am so glad you enjoyed them!

        Reply

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    Ingredients for chocolate zucchini muffins in bowls with labels over each ingredient.
    Double chocolate chip muffin with a bite taken out of it.
    Zucchini chocolate muffin on paper with more zucchini around it.
    Divide the muffin batter between lined muffin cups.
    Baked double chocolate zucchini chocolate chip muffins in a silver muffin pan.
    Baked chocolate muffins with zucchini in a muffin pan with one of the muffins on top of the pan.
    Double chocolate muffins with zucchini
    Wet muffin ingredients mixed in a bowl.