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These chocolate zucchini muffins are rich, moist, and packed with chocolate flavor, yet made with wholesome, kid-friendly ingredients, including shredded zucchini that practically disappears into the batter. Naturally sweetened with maple syrup and freezer-friendly, they’re an easy one to keep on hand for busy mornings and snack time.
Recipe at a Glance
- Rich and chocolatey: muffins that stay incredibly moist
- Whole grain and naturally sweetened: made with white whole wheat flour and maple syrup
- Zucchini-packed: a tasty way to use fresh garden zucchini, with no veggie taste in sight
- Great anytime: perfect for breakfast, snacks, lunchboxes, or a freezer-friendly stash
- Kid-approved: a favorite with babies and toddlers too
- Ready in 30 minutes: makes 10 muffins, with mini muffin and loaf options in the substitutions section
“I was so impressed by these. Great texture and just the perfect amount of sweetness with the 1/3 cup maple syrup. Min is such a talented recipe creator, and I love all the tips, substitutions, etc. Gives me so much confidence to play around with recipes. Thanks Min!” – Katie P
If you’re a chocolate lover, you know chocolate muffins are a glorious thing, and as a pediatric registered dietitian, I love building healthier versions that still deliver. I bake with zucchini often for the texture and nutrition boost, like in these zucchini cookies, baked quinoa, and zucchini carrot muffins, and even in savory dishes like zucchini and corn fritters.
Enjoy these for breakfast, a quick snack, or a lunchbox treat, alongside other favorites like chocolate avocado pudding, banana brownies, and chocolate banana pancakes.
For more ideas, browse this collection of healthy snacks for toddlers and kids.
Table of Contents
Key Ingredients
I am highlighting just the ones that need further explanation. The complete list is in the recipe card below.
- White whole wheat flour: Nutritionally the same as regular whole wheat flour, but lighter in texture and slightly sweeter in flavor.
- Zucchini: Squeeze out as much liquid as you can with a clean kitchen towel or cheesecloth. Measure after squeezing, not before. This is the #1 question readers ask, and it matters because unsqueezed zucchini adds excess water that can make muffins gummy instead of fluffy.
- Unsweetened cocoa powder: Use natural cocoa powder, not dutch-process, for the best flavor, texture, and rise. I personally love Hershey’s.
- Unsweetened applesauce: Store-bought or homemade applesauce both work, and homemade is super easy to make!
- Pure maple syrup (1/3–1/2 cup): Adjust within this range for your sweetness preference. Date syrup is a great no-added-sugar swap.
Substitutions
- Gluten-free: Use a 1:1 gluten free flour like this one or oat flour.
- Dairy-free: Any non-dairy milk (unsweetened almond milk works well) and dairy-free chocolate chips.
- Egg-free: Combine 2 tablespoons ground flaxseed with 6 tablespoons water; let sit 8–10 minutes until gel-like, then use in place of the eggs. You should also try these egg free banana muffins!
- Vegan: Combine the egg-free swap above with a dairy-free milk and dairy-free chocolate chips — all three swaps work together without changing the ratios.
- Mini muffins: Fill mini muffin cups about 2/3 full and bake at the same temperature for roughly 11–13 minutes, checking a few minutes early since mini muffins bake much faster than standard size. Yields about 24 mini muffins.
- Loaf pan: Pour the full batter into a greased 9×5-inch loaf pan and bake at the same temperature for 45–55 minutes, tenting with foil after 30 minutes if the top is browning too quickly. Check with a toothpick starting at 45 minutes.
How to Make Chocolate Zucchini Muffins
Step 1: In a large bowl, stir together the dry ingredients.
Step 2: In a medium bowl, whisk together the wet ingredients.
Step 3: Combine the dry and wet ingredients. Be careful not to over mix! Stir in shredded zucchini and chocolate chips, if using.
Step 4: Divide batter evenly into the muffin cups and bake for 20-22 minutes, or until the inserted toothpick comes out clean.
Expert Tips
- Spoon flour into your measuring cup rather than scooping directly from the bag. Scooping compacts the flour and can add significantly more than the recipe calls for.
- Bring cold ingredients (eggs, milk, applesauce, maple syrup) to room temperature at least 15 minutes before baking for more even mixing and a better rise.
- Adjust maple syrup to taste within the 1/3–1/2 cup range. My kids and I like 1/3 cup; my husband prefers the sweeter end. If you’re in his camp, add a bit more maple syrup and/or chocolate chips.
- Don’t overmix after combining wet and dry ingredients. Mix lightly with a spatula until just combined.
Chocolate Zucchini Muffins FAQs
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.
Use unsweetened natural cocoa powder, NOT dutch-process. Natural cocoa is acidic and reacts with the baking soda for a good rise; dutch-process is alkalized and can leave muffins flatter and denser.
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).
Yes. Thaw it fully first, then squeeze out the extra liquid just as you would with fresh zucchini. Frozen zucchini releases even more water as it thaws, so this step matters even more than usual.
The two most common causes are not squeezing enough liquid out of the zucchini, and overmixing the batter after combining the wet and dry ingredients. Both add excess moisture or gluten development that weighs the muffins down.
More 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
- Non-stick muffin pan
Ingredients
Dry
- 1 1/4 cups white whole wheat flour (150g)
- 1/4 cup unsweetened cocoa powder (25g)
- 1 teaspoon baking powder
- 1/2 teaspoon baking soda
- 1/4 teaspoon salt
Wet
- 1/2 cup unsweetened applesauce (125g)
- 1/2 cup milk
- 1/3-1/2 cup maple syrup
- 2 eggs, lightly beaten
- 1 teaspoon vanilla extract
Fold in
- 1 cup shredded and squeezed zucchini (120g)
- 1/2 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 ;).
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
Adds moisture and sweetness. You can try with ripe banana!
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?
Yes! Hope you enjoy!
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 ?
Hi! If you want to try making it at home, I have a recipe for unsweetened applesauce. If not, you can use mashed banana!
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.
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!
You did it again! Sooooo good! I even tried it in my mini waffle maker and they turned out great!
Ooh!!! Yay!! And I will def have to try these as waffles too!
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!
You’re welcome! I’m so glad that your whole family enjoyed these muffins!
If I’m using mini muffin tins should I reduce the cooking time?
Thanks 🙂
Yes! I would start checking after 15 minutes!
Out of this world! Both me and my little one devoured these 🤤 Thank you so much, Min 🌷
Oh this makes me so happy! Thanks for trying out the recipe!!
Hi Min, thanks for all your helpful recipes! Could you sub banana for applesauce?
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.
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!
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!
Super excited to try! Is this suitable for babies under 1? Thanks! 🙂
Hi! I would hold off until 2 because of cocoa powder and added sugar