These chocolate zucchini muffins are fluffy, fudgy, rich, and perfectly moist with just the right amount of sweetness. They are sure to satisfy your chocolate craving.

Zucchini Chocolate Muffins
Chocolate muffins are a glorious thing. I can always count on chocolate to pick me up when I'm in need of some TLC.
While I could never turn down a super fudgy, chocolate-y, sweet, bakery-style chocolate muffin, it's also in my DNA as a pediatric registered dietitian to come up with healthier versions of those decadent pleasures.
Oftentimes that means combining a healthy dose of fruits, vegetables, and whole grains with some fun!
I absolutely adore baking with zucchini because it adds such great texture and moisture to the final product while boosting nutrition - like in these zucchini cookies, baked quinoa, and zucchini carrot muffins.
And It's such a great way to get extra vegetables into your child's diet as well as yours. Enjoy for breakfast on busy mornings, as a quick snack or treat.
Looking for more healthy chocolate-y recipes? You HAVE to try these chocolate avocado pudding, banana brownies, and chocolate banana pancakes!
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Ingredients


I am highlighting just the ones that need further explanation. The complete list is in the recipe card below.
- White whole wheat flour - It's the same nutritionally as whole wheat flour but is lighter in texture and a little sweeter in flavor.
- Zucchini - Be sure to squeeze out as much excess moisture from the zucchini as you can by using a clean kitchen towel or cheesecloth.
- Unsweetened cocoa powder - Use unsweetened natural cocoa powder. I personally love Hershey's.
- Unsweetened applesauce - can use store-bought or homemade applesauce (super easy to make!)
- Pure maple syrup - you can just how much to add depending on your sweetness preference. Date syrup is a great no added sugar alternative.
- Milk - Preferably whole milk but you can use any milk of choice.
Step-by-Step Instructions

- In a large bowl, stir together the dry ingredients.
- In a medium bowl, whisk together the wet ingredients.
- Combine the dry and wet ingredients. Be careful not to over mix! Stir in grated zucchini and chocolate chips, if using.
- Divide batter evenly into the muffin cups and bake for 20-22 minutes, or until the inserted toothpick comes out clean.
Substitutions
- Gluten-free? Use a 1:1 gluten free flour like this one or oat flour.
- Dairy-free? Any non-dairy milk (e.g. unsweetened almond milk) will work.
- Egg-free? In a bowl, combine 2 tablespoons of flaxseed meal (ground flaxseed) and 6 tablespoons of water. Allow the mixture to sit for 8-10 minutes until thickened like gel-like consistency. You should also try these eggless banana muffins ;).
Tips for Success

- Use a spoon to scoop the flour into the measuring cup rather than scooping the flour out of the container or bag with your measuring cup. Using the latter method, you could end up with a lot more than what you need.
- Take all the cold ingredients out of the refrigerator at least 15 minutes prior to baking. These include eggs, milk, applesauce, and maple syrup.
- I've provided a range for the maple syrup amount so you can decide how sweet you want the muffins to be. The kids and I found â…“ cup to be just enough, but the husband prefers them sweeter. If that's you, you can add more maple syrup and/or chocolate chips.
- After combining the dry and wet ingredients, do NOT over-mix the muffin batter. Mix lightly with a spatula until just combined. Otherwise, you will end up with dense muffins.
Equipment
If you've tried any of my muffin recipes, you know how much I love using this silicone muffin tin because nothing sticks!! There's no need to grease or use muffin liners.
But for those who prefer an alternative, this is my favorite nonstick muffin pan.
Storage
Transfer to an airtight container and keep on the counter for up to 2 days. You can also refrigerate for up to 4 days. Enjoy at room temperature or microwave briefly.
To freeze, I recommend flash freezing. Transfer to freezer-safe bags. Will keep for up to 3 months. Thaw in the refrigerator overnight.
Here's a step-by-step guide on how to store and freeze muffins.
Frequently Asked Questions
Use unsweetened cocoa powder and not dutch-process powder for best flavor, texture, and a good rise.
There's no need! It's soft and will easily grate and blend into the muffin batter. Not to mention it's where most of the nutrients are found!
You can shred in a food processor or use a box grater. If you don't want any visible zucchini pieces in your chocolate muffins, you should finely grate. I personally like to use the large holes so that my kids can see little pieces of vegetables (although they will completely blend in the longer they sit).
The more your child sees foods they are uncertain about, the more likely they are to try, if not today then in the future.
Other Healthy Muffins to Try
Did you make this recipe? Leave a rating below and let me know how you liked the recipe! Your feedback means so much to me!

Chocolate zucchini muffins
Equipment
- Muffin Pan OR
Ingredients
Dry
- 1 ¼ cups white whole wheat flour (150g)
- ¼ cup unsweetened cocoa powder (25g)
- 1 teaspoon baking powder
- ½ teaspoon baking soda
- ¼ teaspoon salt
Wet
- ½ cup unsweetened applesauce (125g)
- ½ cup milk
- â…“-1/2 cup maple syrup
- 2 eggs, lightly beaten
- 1 teaspoon vanilla extract
Fold in
- 1 cup shredded and squeezed zucchini (120g)
- ½ cup chocolate chips (optional)
Instructions
- Preheat oven to 350 degrees Fahrenheit. Grease, line, or use a silicone muffin pan.
- In a large bowl, stir together the dry ingredients.
- In a medium bowl, whisk together the wet ingredients.
- Combine the dry and wet ingredients. Be careful not to over mix! Use a spatula (instead of a whisk) to gently stir together until all the flour is wet. The less you stir the mixture, the lighter and fluffier your muffins will be.
- Stir in grated zucchini and chocolate chips, if using.
- Divide batter evenly into 10 muffin cups and bake for 20-22 minutes, or until the inserted toothpick in the center of the muffin comes out clean. Allow the muffins to cool for 3-5 minutes before transferring to a wire rack to cool completely.
Notes
- Line an airtight container with paper towel. Add the muffins, place another paper towel on top, close the lid, and keep on the counter for up to 2 days. You can also refrigerate for up to 4 days. Enjoy at room temperature or microwave briefly.
- Dairy-free? Any non-dairy milk (e.g. unsweetened almond milk) will work.
- Egg-free? In a bowl, combine 2 tablespoons of flaxseed meal (ground flaxseed) and 6 tablespoons of water. Allow the mixture to sit for 8-10 minutes until thickened like gel-like consistency. You should also try these eggless banana muffins ;).
Andres says
I want to give these a try but we are gluten free. Would all purpose gf flour work or would oat flour work? Are the measurements the same?
Min says
Yes to both and same amount!
Sara elhadad says
Hello looks amazing will definitely try it
I have a question is there a replacement to the apple sauce or can i skip it?
Thank you
Min says
Adds moisture and sweetness. You can try with ripe banana!
Hailey says
Thanks so much for the recipe! Can’t wait to try these..do I need to squeeze the water out of the Zucchini before adding to mixture?
Min says
Yes! Hope you enjoy!
Ameena says
Hi so I don't think we get applesauce where I'm from. Or maybe I've never noticed it. Is there a substitute for applesauce ?
Min says
Hi! If you want to try making it at home, I have a recipe for unsweetened applesauce. If not, you can use mashed banana!
Leona says
Min
Thank you for your most delicious recipes my grandson yums it up!
What can l substitute for white whole wheat flour and how does it affect recipe if l use whole wheat flour.
Min says
Hi! Using all whole wheat flour will make the muffins pretty dense. I would use 3/4 cup all purpose flour and 1/2 cup whole wheat flour!
Abby says
You did it again! Sooooo good! I even tried it in my mini waffle maker and they turned out great!
Min says
Ooh!!! Yay!! And I will def have to try these as waffles too!
Stephanie says
Made these with my toddler and they were a hit! Opted to not use chocolate chips and went with 1/2 cup maple syrup and they were just the right amount of sweetness to be enjoyed by my 2.5 year old and husband. Thanks for the great recipe!
Min says
You're welcome! I'm so glad that your whole family enjoyed these muffins!
Louisa says
If I'm using mini muffin tins should I reduce the cooking time?
Thanks 🙂
Min says
Yes! I would start checking after 15 minutes!
Gal says
Out of this world! Both me and my little one devoured these 🤤 Thank you so much, Min 🌷
Min says
Oh this makes me so happy! Thanks for trying out the recipe!!
Irene says
Hi Min, thanks for all your helpful recipes! Could you sub banana for applesauce?
Min says
Sure! I feel like I'm always using banana in baked goods so thought I'd switch it up haha but also some people don't like the chocolate + banana flavor combo.
Jeanne says
Hi Min! If we can't find white whole wheat flour, can we just do a direct substitution for either AP flour or whole wheat flour? Do we need to change the measurements? Thanks!
Min says
HI yes! You can do all AP flour or half half AP and whole wheat flour. The weight will vary slightly so be sure to use use 1 1/4 cups using the scoop and level method as described in the "tips for success" section!
Cheryl says
Super excited to try! Is this suitable for babies under 1? Thanks! 🙂
Min says
Hi! I would hold off until 2 because of cocoa powder and added sugar