This post may contain affiliate links. Please see our disclosure policy for more details.

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

A direct shot of muffin with a bite taken out.
Want to save this recipe?
Just enter your email and get it sent to your inbox! Plus you’ll get new recipes from us every week!

Chocolate Zucchini Muffin Recipe

If you are a chocolate lover, you know – chocolate muffins are a glorious thing! 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! And here are the best of the best healthy muffins for kids all in one place!

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 these delightful chocolatey zucchini muffins for breakfast on busy mornings, as a quick snack or perfect treat.

Looking for more healthy chocolate-y recipes? You HAVE to try these chocolate avocado pudding, banana brownies, and chocolate banana pancakes!

For more, check out this ultimate list of healthy snacks for toddlers and kids.

Ingredients

All the ingredients laid out on a white background.

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 grated 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

Dry ingredients combined in a glass bowl.

Step 1: In a large bowl, stir together the dry ingredients.

Wet ingredients combined in glass bowl.

Step 2: In a medium bowl, whisk together the wet ingredients.

Dry and wet ingredients mixed along with zucchini.

Step 3: Combine the dry and wet ingredients. Be careful not to over mix! Stir in shredded zucchini and chocolate chips, if using.

Batter transferred to a muffin pan.

Step 4: Divide batter evenly into the muffin cups and bake for 20-22 minutes, or until the inserted toothpick comes out clean.

Substitutions

  • Gluten-free chocolate zucchini muffins: 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 Making the Best Chocolate Zucchini Muffins

squeezed grated zucchini with excess liquid in a bowl.
  • 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 1/3 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

An overhead shot of muffins in a baking pan with shredded zucchini.

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 (pictured above).

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

What is the best cocoa powder to use?

For these muffins use unsweetened cocoa powder and NOT dutch-process powder for best flavor, texture, and a good rise.

Do I need to peel the zucchini?

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!

What is the best way to shred zucchini?

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).

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!

5 from 13 votes

Chocolate zucchini muffins

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.
Prep Time: 10 minutes
Cook Time: 20 minutes
Total Time: 30 minutes
Servings: 10
Want to save this recipe?
Just enter your email and get it sent to your inbox! Plus you’ll get new recipes from us every week!

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 ;).

Nutrition

Calories: 114kcal | Carbohydrates: 22g | Protein: 4g | Fat: 2g | Fiber: 3g | Sugar: 9g
Like this recipe? Rate and comment below!

About Min

Thank you so much for stopping by! I am Min, a Registered Dietitian, a Christ follower, a wife, and a mom to our two miracle babies! Currently, I’m having a ton of fun feeding their tummies and sharing our baby led weaning journey! Follow me on Instagram if interested in seeing daily menu as well as tips and tricks.

Leave a comment

Your email address will not be published. Required fields are marked *

Recipe Rating




31 Comments

  1. 5 stars
    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 🙂

  2. 5 stars
    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.

  3. 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!!

  4. 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?