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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 ;).
Do we measure the zucchini before or after squeezing all the liquid out?
After squeezing!
Hello 🙂 any substitute you can recommend for the apple sauce? Would 2 ripe mashed bananas will work? Thank you
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!
Hi Katie! I’m So glad you loved these muffins as much as do and my goodness thank you so much for such encouraging words! Thank YOU!
I love these. I used 1/2 cup date syrup (aka blended dates) instead of maple, and mashed overripe banana instead of applesauce. The result is a very lightly sweetened, so fluffy, yummy muffin. I made these for a 2 year old who hasn’t been exposed to overly sweet baked goods yet and these are perfect for him. To make these for him when he’s older (or for adults) I’ll add some sweetened chocolate chips. But until then, we are loving these healthy chocolate zucchini muffins 🙂
yay!! thank you for sharing!
Thank you so so much for this recipe! I’ve made these a dozen times already. We opt for 1/3 maple & extra mini chocolate chips on top. A note for storing after: because of how moist these are, I wouldn’t leave countertop for more than 24 hours or 2 days in the fridge. Appreciate all your recipes 🙂
Phenomenal. Made a few changes to use up what I had – banana instead of applesauce (1/2 cup like MJ recommended for someone in the comments), mix of maple syrup and jaggery, 2/3 AP flour and 1/3 whole wheat.
Can’t wait to try your other recipes MJ. Feeding kids should be this good.
Oh yay!! Makes me SO happy to hear this! And thank you for such an encouraging comment :).
Can you make these in a mini muffin tin
You can!
Can u freeze them?
Absolutely – refer to my how to freeze muffins post!
Hi there! If I use bananas instead of applesauce, can I skip the maple syrup as well? And how much bananas should I use if I want to substitute both applesauce and maple syrup? Thank you!!
I haven’t tried so can’t say for certain but I would start with 1/2 cup mashed overripe bananas.
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?
Yes to both and same amount!