Healthy Chocolate Zucchini Muffins

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You will never know these rich and decadent chocolate zucchini muffins are made with healthy ingredients. Enjoy for breakfast, snack time, or dessert!

Healthy Chocolate Zucchini Muffins

Healthy Chocolate Zucchini Muffins

I love zucchini season because I love making zucchini EVERYTHING! Zucchini bread, zucchini cake, zucchini brownies, zucchini pancakes…and the list goes on. You can check out my favorite zucchini recipes here, there are lots of zucchini recipes to choose from, sweet and savory! I usually go sweet and that is the problem. I have been baking up too many loaves of chocolate zucchini bread this month. It’s just so good. I can’t help myself. Well, I decided it was time to make a healthier chocolate zucchini treat…and now you are in for a real treat because they are delicious and I am sharing the recipe TODAY!

These Healthy Chocolate Zucchini Muffins will make you want to jump out of bed so you can eat chocolate for breakfast. They are a great breakfast treat…or you can enjoy them as a snack, or dessert because they basically taste like a chocolate cupcake, but they are healthy-ish! I love them, my kids love them, and I think you will love them too.

Healthy Chocolate Zucchini Muffins Recipe

Chocolate Zucchini Muffin Ingredients

These chocolate zucchini muffins are made with healthy ingredients, but you will never know it because they are so rich and decadent. You will need the following ingredients:

  • White whole wheat flour-you can use whole wheat pastry flour or all-purpose gluten-free flour if you need the muffins to be gluten-free.
  • Unsweetened cocoa powder-use a high quality brand of cocoa for the best chocolate flavor.
  • Baking powder, baking soda, and salt-baking staples that you probably have in your pantry!
  • Unsweetened vanilla almond milk-I love using almond milk, but you can also use buttermilk if you don’t need the recipe to be vegan.
  • Coconut oil-measure the coconut oil when it’s at room temperature, then melt it in the microwave. Let cool for about 5 minutes before using.
  • Pure maple syrup-I use pure maple syrup because it is a natural, unrefined sugar. The flavor is great too! You can use honey, if you don’t need the recipe to be vegan.
  • Large egg-if you need the recipe to be vegan, use a flax egg.
  • Vanilla extract-always use pure vanilla extract. I know it is pricey but so worth it!
  • Zucchini-the star of the show! You will need 2 cups of shredded zucchini (2 small zucchinis or one large zucchini). Don’t squeeze out the liquid or your muffins will be dry! The muffins need the moisture from the zucchini.
  • Chocolate chips-I use Enjoy Life Dark Chocolate Chips for this recipe because they are vegan, gluten-free and made with unrefined sugar. They taste good too, I promise:)
Chocolate Zucchini Muffins

Double Chocolate Zucchini Muffins

Double the chocolate, double the fun, right? You will go crazy for these over the top chocolate muffins. The cocoa powder and chocolate chips team up to create the BEST chocolate muffin! The zucchini keeps the muffins super moist, but you really won’t know you are eating a muffin packed with a vegetable because all you will taste is chocolate goodness!

The muffins are good out of the oven, but I highly recommend you let the muffins cool and sit for a few hours or if you want to make them the day before enjoying, even better. The muffins get even more rich and chocolaty as they sit. I promise, they are worth the wait, you will see what I am talking about if you are patient. And the added bonus? This is a great recipe to make in advance. Make the muffins the night before so you can roll out of bed and enjoy a chocolate zucchini muffin for breakfast! WINNING!

You can freeze the chocolate zucchini muffins. Cool completely and place muffins in a freezer bag or container. Freeze for up to 2 months. Defrost on the counter or reheat in the microwave for 20 to 30 seconds.

More Muffin Recipes:

Easy Healthy Chocolate Zucchini Muffins
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Healthy Chocolate Zucchini Muffins

You will never know these rich and decadent chocolate zucchini muffins are made with healthy ingredients. Enjoy for breakfast, snack time, or dessert!
4.38 from 54 votes


  • 1 1/2 cups white whole wheat flour
  • 1/3 cup unsweetened cocoa powder
  • 1 teaspoon baking soda
  • 1/2 teaspoon baking powder
  • 1/4 teaspoon salt
  • 1/3 cup unsweetened vanilla almond milk
  • 1/4 cup coconut oil, melted and cooled
  • 1/3 cup pure maple syrup
  • 1 large egg (or flax egg)
  • 1 teaspoon vanilla extract
  • 2 cups shredded zucchini
  • 3/4 cup chocolate chips, divided (I use Enjoy Life)


  • Preheat oven to 350 degrees Line muffin tin with paper liners or spray with cooking spray. Set aside.
  • 2In a medium, whisk together flour, cocoa powder, baking soda, baking powder, and salt. Set aside.
  • In a large bowl, stir together almond milk, coconut oil, maple syrup, egg, and vanilla extract. Stir in the shredded zucchini until well combined.
  • Add the dry ingredients to the zucchini mixture and stir until just combined, don’t over mix. Stir in ½ cup of the chocolate chips.
  • Divide batter evenly into prepared muffin cups. Sprinkle remaining chocolate chips over the tops of each muffin. Bake for 20-24 minutes or until a toothpick inserted in the center of a muffin comes out mostly clean. It’s ok if there is a little chocolate from the chocolate chips. The muffins should be set on top and bounce back when lightly touched. Remove from oven and let cool for 10 minutes before serving. Enjoy!


If you need the muffins to be gluten-free you can use all-purpose gluten-free flour. I think the muffins are even better the second day! The muffins freeze well! To reheat, place frozen muffins in microwave for 20-30 seconds.


Calories: 186kcal, Carbohydrates: 26g, Protein: 4g, Fat: 9g, Saturated Fat: 7g, Cholesterol: 14mg, Sodium: 157mg, Potassium: 149mg, Fiber: 3g, Sugar: 11g, Vitamin A: 60IU, Vitamin C: 3.7mg, Calcium: 58mg, Iron: 1.6mg
Keywords healthy

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I'm Maria and my husband is Josh. We share a love of cooking, baking, and entertaining. We enjoy creating recipes that are simple, fresh, and family friendly. We love sitting around the table with good food, good conversation, and good friends and family! Our kitchen is always open!
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    1. have done this recipe twice using vanilla soy milk for the same reason you are mentioning and it works great / would assume vanilla oat milk would do the trick as well.

  1. These are SO INCREDIBLY GOOD!!! love a recipe that is lightened up and full of healthy ingredients!! Thank you!!

    1. I don’t unless the zucchini is HUGE and super watery, then I squeeze it out a little. But don’t squeeze it out too much or the muffins will be dry.

  2. 1 star
    I really wanted to like these, but I started to notice things going downhill once I put in the dry ingredients. The mixture was far too dry, so I added more milk (oat) and it was less dry but way too bitter. I added extra chocolate chips which cut the bitterness but not enough. Will not make again.

  3. Looks great but I don’t use Almond Milk or Coconut Oil…do you have any options I can substitute for those two?

    I only use real whole milk and Coconut Oil and I don’t not get along…

    1. I used avocado oil when I made them today and it worked great! They were so good 🙂

  4. 1 star
    This recipe did not work for me! I followed the recipe with exact measurements only changing coconut flour in place of the white wheat flour. The batter was way, WAY too dry- like sandy gravel. I wasted a lot of ingredients and got nothing edible from my time or efforts. Disappointed!

    1. It’s not fair to rate this with 1 star when you made a terrible substitution… Coconut flour is known to soak up tons of moisture.

  5. 4 stars
    I made this recipe with a gluten free flour mix, regular 2% milk, and egg. Turned out great, not too sweet, and the chocolate chips make it delicious! My kids love them, especially my picky middle child. Will be making these again!

  6. 5 stars
    Recipe worked great for me! I love that it uses 2 cups of zucchini- the more the better, as I have loads from my garden

  7. For the cocoa powder, almond milk, and maple syrup it says “&frac13” for the measurement for some reason. What’s the actual measurement for these ingredients?


    1. I haven’t tried the recipe with almond flour and it has a different texture so I don’t recommend an even swap. You can use an all-purpose gluten-free flour. I like Cup4Cup.

  8. Hi there i was wondering what white whole wheat flour is? i can not find it anywhere where i live! I did make this recipe with gluten free flour, however tasted a little sandy? The muffins were wonderful i just prefer adding more sweetness is there something you can suggest so my picky toddler loves this?

  9. 4 stars
    Hi there i was wondering what white whole wheat flour is? i can not find it anywhere where i live! I did make this recipe with gluten free flour, however tasted a little sandy? The muffins were wonderful i just prefer adding more sweetness is there something you can suggest so my picky toddler loves this?

    Also, how much gluten free flour do you suggest using?

    1. If you can’t find white whole wheat flour, you can use regular flour or whole wheat flour. White whole wheat just has a lighter texture than regular whole wheat. If you want to use gluten-free flour, I like Cup4Cup. Use the same amount.

  10. Thanks for the recipe! It turned out great. Have you ever used frozen zucchini in this recipe? If so, do you drain the water after thawing? I have a bunch of zucchini that I like to freeze in 2 cup containers. I love that this recipe uses 2 cups of zucchini! Thanks in advance!

    1. Have you tried making this in a standard loaf pan rather than muffins? Just wondering if this would work since most muffins recipes can be made in a standard loaf pan as quick bread and vice versa. Thanks

  11. 1 star
    Horrible !! I followed directions exactly and it came out so thick like cookie dough . They don’t taste that good either .

    1. 5 stars
      These are delicious! My boyfriend, who typically doesn’t like healthier baking recipes, loved them. I used just 1/8 cup chocolate chips on the tops and added a little bit of coarse salt instead. I’ll definitely make them again!

  12. 5 stars
    Moist and chocolaty!
    I will grate the zucchini more finely next time. The coarse grate was ok but a finer grate would mix better.

  13. 5 stars
    Absolutely, hands down, the BEST chocolate zucchini muffin recipe I’ve tried!!!! I’ve found my keeper!!! THANK YOU!

  14. 5 stars
    So good! We used some protein powder as well for a little added nutrition. Great way to hide some veggies for picky eaters. 4 year old approved!

  15. Subbed olive oil for coconut oil (didnt realize I was out!) they turned out SO delicious!! Thanks for the recipe.

  16. 5 stars
    I made these muffins today on a cool rainy day. I had to make some substitutions as I did not want to go out in inclement weather. I used oat milk, olive oil, almond extract and unfortunately I did not have any chocolate chips so I had to forego that. Muffins baked up moist and yummy. Thank you for this easy and tasty recipe that was simple to prepare.

  17. for some reason the muffins kinde got glued to the muffin paper. They break apart when i am pulling the paper off of them cause they got stuck on them so much. I am not sure why this happened. Can you explain this?
    They taste good tho. I used my immersion blender wand to puree the zucchini cause the last time i made zucchini muffins all the zucchini gelled to the bottom the the muffins as they were cooking. But these are good.