Healthy Double Chocolate Zucchini Muffins

Healthy chocolate zucchini muffins made with whole wheat flour and no butter or refined sugars (besides chocolate chips). You’re going to love these perfectly moist, insanely delicious double chocolate muffins!

Prep Time
10 mins
Cook Time
25 mins
Total Time
35 mins

Listen up party people. Zucchini week is about to be blowing up your gardens and therefore I plan on blowing your mind with my very famous annual #AKZUCCHINIWEEK. Mark your calendars for the week of August 5th where we celebrate all things zucchini with breakfast, sweets, savory meals and of course AN EPIC CAKE.

healthy chocolate zucchini muffin

Let me just say that if you’re thinking that you would never put zucchini in a baked good, it’s time to get out of your comfort zone because these muffins are MIND-BLOWING and full of chocolate love with zero zucchini taste.

I love when vegetables can taste like chocolate, don’t you?

Chocolate zucchini muffin

After all, remember my skinny banana chocolate chip zucchini muffins from a few summers ago? Or how about these chunky monkey zucchini muffins? Probably one of my favorite muffins on my blog.

I say that about every muffin I put on this blog though, so think what you will.

This recipe just so happens to be originally from 2014, then retested last year to perfection. I like to republish these chocolate zucchini muffins every so often to remind you just how delicious they are.

healthy chocolate zucchini muffin

Chocolate zucchini muffin ingredients

You would think that the average zucchini bread would be healthy, but most recipes call for more than a cup of sugar and at least a 1/2 cup of oil. Healthy fats are absolutely wonderful but I’d rather put them on top of my muffin (like a big scoop of peanut butter). So I thought I’d try my best to make healthy chocolate zucchini muffins with nutritious, good-for-you ingredients, yet still keep them tasting amazing and moist. Here’s what you’ll need:

Zucchini: Of course, this veggie adds an insanely amount of moisture to the muffins. Shred it up, squeeze it of all excess moisture with a paper towel, then use it in this recipe.

Banana or applesauce instead of lots of oil: Keeps the muffins moist and adds natural sweetness. I prefer to use mashed ripe banana, but applesauce will also work well.

Honey or pure maple syrup instead of sugar: I love using all natural sweeteners in baking and both honey and pure maple syrup will work in this recipe.

Almond milk: Delicious and dairy free. I’m cool with that.

Egg: I like to use an egg for a boost of protein, but I think a flax egg would work if you are trying to keep these vegan.

Whole wheat pastry flour: Probably the best wheat flour out there. You can’t even tell these muffins are whole-grain. You can also use a gluten free all purpose flour if you prefer.

Unsweetened cocoa powder: cocoa powder is my favorite way to boost chocolate flavor in recipes. I like using this brand. If you want a more nutritious alternative, you can try cacao powder (I use it all the time!)

Holding a healthy chocolate zucchini muffin

These chocolate zucchini muffins would be perfect for breakfast, an afternoon treat, or even dessert. You can even bake these as bars or as a bread, but of course you’ll need to adjust baking times. Dollop these with a big tablespoon of peanut butter and prepare to fall in love!

See how to make these chocolate zucchini muffins:

If you make this recipe, be sure to leave a comment below and rate the recipe! You can also snap and picture and post it on Instagram using the hashtag #ambitiouskitchen. xo!

Healthy Double Chocolate Zucchini Muffins

4.87 from 36 votes
Course Breakfast, Dairy Free, Muffins
Keyword chocolate zucchini muffins
Prep Time 10 minutes
Cook Time 25 minutes
Total Time 35 minutes
Serves 12
Zucchini chocolate muffins get a healthy makeover! Made with whole wheat flour and no butter or refined sugars. You're going to love these perfectly moist, insanely delicious muffins!


  • 1 1/4 cup whole wheat pastry flour or white whole wheat flour
  • 1/3 cup unsweetened cocoa powder
  • 1 teaspoon baking soda
  • 1/4 teaspoon salt
  • 2 tablespoons coconut oil, melted and cooled
  • 1/3 cup honey, agave nectar or pure maple syrup
  • 1 teaspoon vanilla
  • 1 egg
  • 1 cup shredded zucchini (about 1 medium)
  • 1 ripe mashed banana (or you can use 1/4 cup unsweetened applesauce)
  • 1/2 cup unsweetened vanilla almond milk
  • 1/2 cup regular or mini chocolate chips, dairy free if desired


  1. Preheat oven to 350 degrees F. Line 12 cup muffin tin with cupcake liners and generously spray inside of liners with nonstick cooking spray.
  2. Squeeze shredded zucchini of excess water with a paper towel. This is important, so don’t forget!
  3. In a medium bowl, whisk together flour, cocoa powder, baking soda, and salt; set aside.
  4. In the bowl of an electric mixer, add coconut oil, honey/maple syrup, vanilla, egg; mix on medium-low until smooth and well combined. Add in zucchini, banana (or applesauce) and almondmilk; mix again. Slowly add in dry ingredients and mix until just combined. Gently fold in chocolate chips.
  5. Evenly divide batter into prepared liners. Bake 22-25 minutes or until toothpick inserted into middle comes out clean. After 5 minutes, remove muffins and transfer to wire rack to finish cooling. Enjoy!

Recipe Notes

To keep muffins dairy free, use dairy free chocolate chips.

I love adding a few extra chocolate chips (2-3) on top of each muffin before baking to make them look pretty, but it's up to you!

Servings: 12 muffins
Serving size: 1 muffin
Calories: 160kcal
Fat: 6g
Carbohydrates: 25g
Fiber: 2.3g
Sugar: 14g
Protein: 3.4g

If you like this recipe, you might also like:

Healthy Chocolate Zucchini Cake with Avocado Chocolate Frosting

Healthy Carrot Cake Muffins with Cream Cheese Glaze

Grain Free Chocolate Chip Peanut Butter Zucchini Bread (2 different ways!)

Chocolate zucchini muffin

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