Super Healthy Chocolate Zucchini Muffins (Vegan & Refined Sugar Free)

by | Jul 12, 2019 | Breakfast, Chocolate, Dairy-Free, Desserts, Gluten-Free, Low Sugar, Nut-Free, Recipes, Vegan, Vegetarian, Whole Grains | 35 comments

Inside Scoop: Hide your veggies in chocolate with these healthy chocolate zucchini muffins.

This recipe was submitted by Tara Thorne, Registered Holistic Nutritionist with a focus on helping busy mums take control of their health and happiness.

Fudgey, chocolatey, and loaded with all the right kind of healthy ingredients (including veggies), these super healthy Chocolate Zucchini Muffins will make all your muffin, and all your chocolate dreams come true!

There’s something about sneaking zucchini into foods, and you know that we love a good chocolate recipe, that’s why when Tara Thorne handed over this recipe for these Healthy Chocolate Zucchini Muffins, we were ecstatic to whip up a batch. As a matter of fact, we make these muffins on the regular. They are perfect for breakfast, snacking, kiddos and when you’re busy and on-the-go. They really beat the heck out of those sugar laced Tims or Starbucks muffins, and are much better for you…. plus… all the chocolate!

One of our favourite things about these little healthy chocolatey zucchini muffins of joy is that they contain a load of gut loving ingredients. You have whole grains (which are loaded with fiber), apples (which contain prebiotics) and flax seeds (which also contain prebiotics, as well as anti-inflammatory fats).

If you want to learn more about gut loving foods, make sure you download your Top 25 Gut Healing Foods List here, and learn more about how to apply the best prebiotic and probiotic rich foods to your diet. Snatch a copy here:


Not only do these Healthy Chocolate Zucchini Muffins contain gut-loving ingredients, but these are a sneaky little way to get some of your daily dose of veggies in.

Hiding veggies in chocolate? You bet your cute butt we would.

So get in on these healthy chocolate zucchini muffins today, because they:

  • Contain whole grains
  • Have no refined sugar
  • Contain vegetables
  • Double chocolate….. of course!
  • Contain fiber
  • Contain healthy fats
  • Are chocolaty, fudgey and oh so delicious

Don’t mind us, we’ll be over here snacking out on all the chocolate! Oh yeah, and speaking of chocolate, if you’re digging this double dose, you might want to check out our No Bake Chewy Peanut Butter Chocolate Cookies  they’re one of our favs!

What do you think about Healthy Chocolate Zucchini Muffins? Let us know in the comments below.


4 from 3 votes

Healthy Chocolate Zucchini Muffins

Hide your veggies in chocolate? Okay! These Super Healthy Chocolate Zucchini Muffins are a total win!
Course Breakfast, Dessert, Snack
Cuisine Healthy
Keyword healthy chocolate zucchini muffins
Prep Time 10 minutes
Cook Time 20 minutes
Resting time 1 minute
Total Time 30 minutes
Servings 12
Calories 159 kcal


  • 1 1/4 cup whole wheat flour or spelt, oat if using GF
  • 1/3 cup cacao powder unsweetened
  • 1 tsp baking soda
  • 1/4 tsp salt
  • 3 Tbsp coconut oil melted
  • 1/3 cup maple syrup or honey
  • 1 tsp vanilla
  • 2 Tbsp flax
  • 1 cup shredded zucchini about 1 medium
  • 1/3 cup unsweetened applesauce
  • 1 cup non-dairy milk alternative e.g. almond, cashew, coconut
  • 1/2 cup chocolate chips dark chocolate, dairy free


  1. Preheat oven to 350 degrees F.
  2. Line 12 cup muffin tin with cupcake liners.
  3. Shred the zucchini and use paper towels to squeeze out excess water. Important step!
  4. Whisk together flour, cocoa powder, baking soda, and salt; set aside.
  5. In separate bowl mix together melted coconut oil, maple syrup/honey, vanilla, flax, zucchini, applesauce, milk alternative and chocolate chips.
  6. Slowly and in batches add dry ingredients to wet.
  7. Mix until just combined. THE MIXTURE WILL BE RUNNY! This is a-ok. In fact, it's the reason these puppies come out so delectably moist.
  8. Evenly spoon into muffin liners.
  9. Bake for about 20 minutes. Muffins are done once a toothpick inserted into the middle comes out clean.
  10. Enjoy!

Recipe Notes

* Store muffins in an air-tight container in the fridge

Tara Thorne

Tara is a Registered Holistic Nutritionist with a diploma from the Canadian School of Natural Nutrition. She also has training from the Institute for Functional Medicine, specifically in hormones and is currently finishing up studying to become a Certified Functional Nutrition Coach. Tara is an expert at interpreting the DUTCH comprehensive hormone test and MTHFR and nutrigenomics, having studied methylation and clinical nutrigenomics at the Seeking Health Educational Institute. Tara’s practice focuses on helping busy mums navigate the overwhelm and confusion surrounding how to live healthfully in a hectic world by providing evidenced-based functional nutrition and lifestyle strategies. She is a mummy of two, an entrepreneur and a writer who writes for publications around the globe with a specific focus on nutrition.

See what Tara is up to by visiting her business finding her on Facebook, Instagram or Pinterest.

Naughty Nutrition

Naughty Nutrition


  1. Toni

    Just made this with my two young boys (who are extremely picky and have a ton of food allergies) not only was the recipe extremely easy for us to follow but the muffins came out DELISH! Thank you!

    • Naughty Nutrition

      That is awesome Toni 🙂 Glad everyone enjoyed it!

  2. Christina

    These look delicious! Do you think they would work as mini muffins? I am guessing I would just reduce the bake time.

    • Naughty Nutrition

      Hi Christina, I would just reduce by about 5 minutes. You’re totally right.

  3. Clarese

    I’m in the process of making them but when you said add the dry mixture in batches. I don’t understand. The end mixture is not runny at all

    • Naughty Nutrition

      thats good! its just easier to mix in slowly =) How were they?

  4. Tai

    Just to clarify, the flax seeds aren’t made into flax eggs, they’re just mixed into the batter, right? Can’t wait to try this!! 🙂

  5. Isabelle

    These look so tasty! Do you think it would work using almond flour? 🙂

    • Naughty Nutrition

      Hi Isabelle! Of course, you can substitute any flour of your choice.

    • Rachel borowiec

      I’m excited to try these! Is the nutrition info for 1 muffin?

  6. Laina

    what if I only have regular flour? is the measurement the same ?

    • Naughty Nutrition

      Hi Laina! Yes same measurement!

  7. Jody

    Hi – by “flax”are you referring to flax seeds? or ground flax seeds?

    • Naughty Nutrition

      Ground flax!

  8. Pam

    These are soooo good. I just made these. I had no flax seed so they were not added. I had to bake my muffins for about 45 minutes.
    Just a FYI be sure to spray your paper liners if they not parchment as my muffins stuck to my liners and sadly wasted a lot of the cupcake ?
    Next time I make these ( cause I will !!) I think I’d like to try adding some shredded coconut.

    • Naughty Nutrition

      Glad you enjoyed these Pam! And…great tip!

    • Naughty Nutrition

      Glad you loved these!

  9. Amy

    I make these regularly, they are AMAZING! I substitute chia seeds for the flax (same quantity) and sometimes use olive oil instead of coconut oil. And I use 100g of Lindt dark chocolate block chopped roughly instead of choc chips. Delicious every time. I also discovered a great trick to squeeze out the water from the shredded zucchini is to use coffee filters to wring out the water if you don’t have a dishtowel/special cloth. Works like a charm!

  10. Rima

    Can I use 2% milk instead of non diary milk alternative? Still one cup?

  11. Jennifer Palmieri

    Has anyone tried using almond flour instead of oat? I can’t have oat , rice, or regular flour.

  12. Christina


    Do I use the flax seeds to make a flax eggs or do I just add to the batter?

  13. Linda

    Is the shredded zucchini measured before or after squeezing the water out?

    Can I use a combination of oat and almond flour?

    • Naughty Nutrition

      Yes you can use either oat or almond flour, and the zucchini is measured after the water is squeezed!

  14. Valentina

    Hi there ! Thank you for the wonderful recipe
    Would it be possible to not use the flax seed ? Or would it change the texture

  15. Lupe

    Have you ever frozen and defrosted these? Wondering if they would get dried out.

    • Sherry Parker

      What can you use instead of applesauce? I have an allergy to apples, banana too.

  16. Suzanne

    This looks so good! What a great way to sneak some veggies to the kids!

  17. Vanessa

    Thanks of sharing! Does it keep long?

  18. Chrissy

    What time would you bake this for if using a loaf pan to make it a loaf cake instead?

  19. Emma

    Hi! I was about to start making these but could you pleace specify if the cups are American or English? It’s a quite big difference and I couldn’t find the info in other tabs either. Thanks! 😀

    • Naughty Nutrition

      They should be the same! American though 🙂

  20. Sonya

    I made these for my family yesterday morning and everyone loved it! My family had eaten all of them by the time I went for seconds! I’m going to make them again today or tomorrow, and was wondering if I made a double batch if I could freeze some of the batter? These are definitely a new family favorite. Thank you!

  21. Elise

    These were not my favorite. If it weren’t for the chocolate chips, they’d be quite bland. Also didn’t rise very much, so they were pretty close textured and kinda gummy, even after being baked for longer than the recommended time.

  22. Joyce Watson

    Can oatmeal be used instead of any flour choice

    • Sam

      Yes you can use any other flour (She answered this earlier) 🙂


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