Healthy Chocolate Zucchini Muffins

Jump to Recipe

This post may contain affiliate links. Please read our disclosure policy.

The best healthy chocolate zucchini muffins recipe! They’re made with nutritious ingredients (like Greek yogurt, oat flour and lots of zucchini), are moist, chocolatey and can be made gluten-free. Plus, they freeze well for a quick healthy breakfast you can grab on the go! 

front view of a healthy chocolate zucchini muffin with chocolate chips


I really enjoy making recipes with sneaky veggies. I love baking with zucchini, spinach, carrots, etc. to make healthy treats my kids love eating! These Healthy Chocolate Zucchini Muffins are the whole package. They are loaded with zucchini, full of fiber, rich in protein, and have a deep chocolate flavor! 

The combination of oat flour and all-purpose flour makes them light, fluffy and nutritious – and they can easily be made gluten-free! The addition of Greek yogurt adds protein. Two heaping cups of zucchini packs them full of nutrients.  Plus, you can earn serious cool-mom points by letting your kids eat chocolate for breakfast.

front view of a stack of two healthy chocolate zucchini muffins with chocolate chips

Healthy Chocolate Zucchini Muffins: Ingredients & Substitutions

overhead photo of the ingredients in this Healthy Chocolate Zucchini Muffins recipe
  • Old-Fashioned oats. You can substitute oat flour (in a 1:1 ratio, so in this recipe 1 1/2 cups) for the old-fashioned oats. You can also use solely all-purpose flour or gluten-free all-purpose flour. 
  • All-purpose flour.  1:1 gluten-free baking flour can be substituted to make these chocolate zucchini muffins gluten-free. You can also use all oat flour, but just know the muffin texture won’t be as tall and fluffy. Whole wheat pastry flour is another great substitution for all-purpose flour too.
  • Greek yogurt. Any plain or vanilla Greek yogurt will work well in this recipe. To make these chocolate zucchini muffins dairy-free, simply use a dairy-free Greek yogurt.
  • Granulated sugar.  Any granulated sugar works well in this recipe, including brown sugar or coconut sugar for a refined-sugar free option.
  • Honey. maple syrup can be used in place of honey.
front view of a Healthy Chocolate Zucchini Muffin with chocolate chip
Chocolate Zucchini Muffins

How to make Healthy Chocolate Zucchini Muffins

These healthy chocolate zucchini muffins are easy to make in a blender (and you can also make them without)! We’ll walk through the process step-by-step, and don’t forget to watch the video!

Use a Vitamix

This is another recipe that deepens my love for my Vitamix. You can take oatmeal, zucchini and a bunch of other good-for-you ingredients and create muffins that are smooth, slightly sweet, and blissfully chocolatey.  Zucchini, where? Zucchini, who? Be sure to check out my Vitamix Buying Guide!

Make Oat Flour

The first step in this healthy chocolate zucchini muffin recipe is to make the oat flour. If you regularly purchase oat flour, then simply use that and skip this step. I always make my own because it costs less and I always have oatmeal on hand. 

To do this, simply put oatmeal in the container of your Vitamix (or another high-powered blender) and blend for 15-30 seconds until it resembles flour. 

two overhead photos showing how to make oat flour to make healthy chocolate zucchini muffins

Combine Dry Ingredients

Transfer the oat flour to a medium bowl and combine it with the rest of the dry ingredients and stir to combine. Set aside to add to the recipe later. 

two overhead photos showing how to make healthy chocolate zucchini muffins - mixing the dry ingredients

Blend Wet Ingredients

Next, blend together the wet ingredients until a homogenous (smooth, uniform throughout) mixture forms. It will be green at this point because you haven’t added the cocoa powder yet.  You can also use a food processor.

If you don’t have a blender/food processor

Mash the bananas, add all the rest of the wet ingredients except for the zucchini. Then proceed with the rest of the recipe, and add the zucchini in at the very end after all the rest of the ingredients have been mixed together by hand. 

two overhead photos showing how to make healthy chocolate zucchini muffins  in a blender- blending the wet ingredients including zuchcini

Add vanilla & sugar

Place the vanilla and sugar into the blending container and blend until the sugar is dissolved. 

Add dry ingredients

Next, add the dry ingredients to the blender and blend until the mixture is smooth. 

two overhead photos showing how to make healthy chocolate zucchini muffins  in a blende - adding the dry ingredients

Add chocolate chips

One the mixture is smooth, add the chocolate chips and stir by hand. 

two overhead photos showing how to make healthy chocolate zucchini muffins  in a blender- adding chocolate chips

Pour into muffin pan & bake

Next, scoop about 1/4 cup of the prepared batter into each well of a greased muffin tin. Bake until the muffins are set and spring back when touched, and a cake tester inserted in the center comes out clean. You can use muffin liners if you prefer.

two overhead photos showing how to make healthy chocolate zucchini muffins - before and after baking in a muffin tin

Remove and cool

Release & remove the chocolate zucchini muffins from the muffin pan and transfer them to a wire rack to cool before eating. 

Serve

Serve these healthy chocolate zucchini muffins with your favorite fruit for a delicious breakfast! Here are some suggestions of spreads that taste great on top of these muffins!

front view of healthy chocolate zucchini muffins on a wire cooling rack

To store:

Store in an airtight container in the refrigerator for 5-7 days.

To freeze:

To freeze, let the muffins cool to room temperature. Then transfer them to an airtight container and store in the freezer for up to 2 months. Reheat in the microwave or oven on low heat.

front view of 6 Healthy Chocolate Zucchini Muffins with chocolate chips

Recipe FAQs

Do you peel zucchini for muffins.

No! Do not peel zucchini to make these healthy chocolate zucchini muffins. The skin contains many nutrients, so leave it on!

How do you store zucchini muffins?

Store in an airtight container at room temperature for 3-5 days, in the refrigerator for 1 week, or in the freezer for up to 3 months.

How many zucchini is two cups grated?

Two cups of grated zucchini equals about two small/medium zucchinis. 

overhead view of a healthy chocolate zucchini muffin cut in half so the inside is visible

If you make and love our recipes, it would mean so much to me if you would leave a comment and rating! And don’t forget to follow along with us on Instagram, Pinterest, Facebook, and Youtube – be sure to tag @joyfoodsunshine and use the hashtag #joyfoodsunshine so we can your creations!

Healthy Chocolate Zucchini Muffins

Laura
The best healthy chocolate zucchini muffins recipe! They're made with nutritious ingredients (like Greek yogurt, oat flour and lots of zucchini), are moist, chocolatey and can be made gluten-free. Plus, they freeze well for a quick healthy breakfast you can grab on the go! 
5 from 23 votes
Course Breakfast, Snack
Cuisine American
Servings 16 muffins
Calories 133
Prep Time5 minutes
Cook Time30 minutes
Total Time35 minutes

Ingredients 
 

Instructions 

  • Preheat oven to 375 degrees F. Grease two 12-cup muffin tins and set aside.
  • Add 1 1/2 cups of oats to your blender (Vitamix) and blend until ground into a fine flour. Remove from blender and put in a medium bowl.
  • Mix in dry ingredients (oat flour, all-purpose flour, cocoa powder, baking powder, baking soda, cinnamon and salt) and set aside.
  • Add zucchini, Greek yogurt, sugar, banana, and honey to your blender and blend until smooth.
  • Add vanilla and eggs and blend on low speed until just combined.
  • Add dry ingredients and blend until combined.
  • Mix in chocolate chips by hand (do not blend)!
  • Pour batter into prepared muffin pan, making sure each well is only 3/4 full.
  • Bake at 375 for 20-25 minutes or until the tops are set and spring back when touched. A toothpick inserted in the center should come out clean or with very few crumbs.
  • Let sit in the muffin pan on a cooling rack for 5 minutes.
  • Run a spoon around each muffin to release from the pan and transfer to a wire rack to cool.

Video

Notes

Ingredient Substitutions

  • Old-Fashioned oats. You can substitute oat flour (in a 1:1 ratio, so in this recipe 1 1/2 cups) for the old-fashioned oats. You can also use solely all-purpose flour or gluten-free all-purpose flour. 
  • All-purpose flour. A 1:1 gluten-free baking flour can be substituted to make these chocolate zucchini muffins gluten-free. You can also use all oat flour, but just know the muffin texture won’t be as tall and fluffy. Whole wheat pastry flour is another great substitution for all-purpose flour too.
  • Greek yogurt. Any plain or vanilla variety will work well in this recipe. To make these chocolate zucchini muffins dairy-free, simply use a dairy-free Greek yogurt.
  • Granulated sugar.  Any granulated sugar works well in this recipe, including brown sugar or coconut sugar for a refined-sugar free option.
  • Honey. maple syrup can be used in place of honey.

If you don’t have a blender/food processor

Follow the recipe as written, but instead of putting the wet ingredients into a blender, Mash the bananas into a large bowl. Then add all the rest of the wet ingredients except for the zucchini and stir to combine. Proceed with the rest of the recipe, and add the zucchini at the very end after all the rest of the ingredients have been mixed together by hand. 

To store:

Store in an airtight container in the refrigerator for 5-7 days.

To freeze:

To freeze, let the muffins cool to room temperature. Then transfer them to an airtight container and store in the freezer for up to 2 months. Reheat in the microwave or oven on low heat.

Nutrition

Serving: 1muffin | Calories: 133kcal | Carbohydrates: 24g | Protein: 4g | Fat: 3g | Saturated Fat: 1g | Cholesterol: 22mg | Sodium: 169mg | Potassium: 182mg | Fiber: 2g | Sugar: 11g | Vitamin A: 78IU | Vitamin C: 3mg | Calcium: 47mg | Iron: 1mg

Nutrition information is automatically calculated, so should only be used as an approximation.

Did you enjoy this recipe? Have a question? Leave a comment below!

try these recipes




latest recipes

Post a Comment or Ask a Question!

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

Recipe Rating




42 Comments

  1. 5 stars
    My 6 yo grandson found this recipe on line! We had all the ingredients and made it together! It is fairly easy and super yummy! One recipe made 24 mini muffins and 6 regular sized muffins. My mini muffins were done in 15-17 minutes. The regular sized were done in 20-22 minutes. Thanks for such a healthy, delicious recipe!

  2. 5 stars
    Absolutely love this recipe. I really appreciate the nutritional facts and the notes of substitutions as well since I am vegan! Thank you so much!!

  3. 5 stars
    I bake these last night!! Great recipe it’s a keeper! Even my husband liked them, thank you so much. Your recipes are exactly as posted.

  4. 5 stars
    Omg — my stomach was legit growling as I read this post! I *love* blender baking recipes. What a genius idea to use zucchin! I can’t wait to try these. Thanks so much for sharing.

  5. Hello dear, I have just made this recipe and am so disappointed!! They were looking so nice and risen in the oven, but as soon as I brought it out, suddenly they all flattened to the bottom of the cups!!!! 🙂 why do you think this happened?

    1. If your baked goods deflate like that it likely means they weren’t baked completely. A completely baked muffin will not deflate.

  6. Ooh la la… :). I love how zucchini is disguised so well in chocolate. These are probably some of the most beautiful muffins I’ve ever seen.

  7. 5 stars
    Delicious! I didnt have any almond meal on hand so I upped the amount of oat flour and the muffins were still very tasty. I’m a big fan of anything with chocolate and banana, and these did not disappoint.

  8. 5 stars
    Made a double batch since I bought WAY TOO MANY yellow squash at the Farmer’s Market! Left out the honey and substituted gf flour for the almond meal (didn’t have any). Added extra cinnamon and cocoa. Superb! Even my non-veggie-eating brother enjoyed them. Thank you for your healthy recipe.

    1. Thank you for stopping by to let me know that you enjoyed this recipe! We love it and I’m so glad that you made a believer out of your brother! 😉

  9. 5 stars
    These look delicious! I’m looking forward to giving them a try, Pinned 🙂