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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! Plus, they are gluten free!

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. Don’t you think? It’s like this magic ingredient that is hidden in the most delicious sweet treats like in this Zucchini Banana Bread and Zucchini Cake.
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!

Why you’ll love this 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
- 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
- Salt
- Olive oil – you can also use coconut oil or melted butter

How to make healthy chocolate zucchini muffins
- Prepare the zucchini: shred the zucchini using a box grater then place it into a clean kitchen towel and squeeze the extra moisture out of it. Quite a bit should come out. Set aside.
- Mix up the dry ingredients: almond flour, cocoa powder, baking soda, and salt in a medium size mixing bowl.
- Mix up the wet ingredients: almond butter, applesauce, egg, maple syrup, vanilla extract and milk in a separate medium size mixing bowl.
- Combine the wet and dry ingredients and mix well into one bowl, then fold in the shredded zucchini and chocolate chips.
- Bake: Divide the batter evenly between 12 muffin cavities of a 12-cup lined muffin pan and bake at 400 degrees F for 22-25 minutes.
- Serve: Remove the chocolate zucchini muffins from the oven, let them cool and enjoy!







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.
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.
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.

FAQ
In this recipe, you do have to squeeze the extra water out of the zucchini.
Once the 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.
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!
Print
Chocolate Zucchini Muffins – Gluten Free
- Total Time: 27 minutes
- Yield: 12 1x
- Diet: Gluten Free
Description
Chocolate zucchini muffins that are so fudgy and decadent and made from healthy, whole ingredients. Hearty zucchini, healthy almond butter and luscious dark chocolate make these muffins the best healthy muffins that even your kids will go crazy for! Gluten free and refined sugar free!
Ingredients
- 1 + ¼ cup blanched almond flour
- ā cup cocoa powder – unsweetenedĀ
- 1 teaspoon baking soda
- ½ teaspoon kosher saltĀ
- 1 large egg – lightly whisked
- ā 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
- ā cup chocolate chips – plus more for topping
Instructions
- Preheat the oven to 400 degrees F and line a 12-cup muffin pan with muffin liners. Ā Set aside.Ā
- Prepare the zucchini: shred the zucchini using a box grater. Ā Place the shredded Zucchini into a clean kitchen towel and wring out the extra water from the zucchini. Set aside.Ā
- In a medium size mixing bowl, mix up the dry ingredients: almond flour, cocoa powder, baking soda and salt.
- In a separate mixing bowl mix up the wet ingredients: egg, maple syrup, applesauce, almond butter, milk, olive oil, vanilla extract.
- Combine the wet and dry ingredients and mix well then fold in the shredded zucchini and chocolate chips.
- Divide the batter evenly between 12 muffin cavities of a 12-cup lined muffin pan and bake at 400 degrees F for 22-25 minutes.
- 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.
- 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: 5 minutes
- Cook Time: 22 minutes
- Category: Healthy Breakfast Ideas
- Method: Baked
- Cuisine: American
Keywords: chocolate zucchini muffins, chocolate chip zucchini muffins, zucchini muffins, gluten free chocolate zucchini muffins
Can I use oat flour? I can’t have Almond flour
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.
Hi,
Could I use something different in place of applesauce?
Thanks
Hi Protima, You could use canned pumpkin or plain Greek yogurt in place of the applesauce.
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?
★★★★
Can you replace the almond butter with something else?
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.