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! 

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.

Healthy Chocolate Zucchini Muffins: Ingredients & 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.  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.

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. 

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. 

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. 

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. 

Add chocolate chips

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

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.

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!

• Homemade peanut butter tastes amazing on these healthy chocolate zucchini muffins. 
• Slather on some homemade cinnamon honey butter. 
• A dollop of this homemade vanilla almond butter tastes amazing! 

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.

Recipe FAQs

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!

More Zucchini Recipes

Here are a few more of our favorite zucchini recipes!

• We love muffins around here. Some of our favorites featuring zucchini are: paleo zucchini muffins, carrot zucchini muffins, and these pumpkin zucchini muffins. 
• This chocolate zucchini cake with a fudgy chocolate ganache is seriously the best. 
• Who doesn’t love healthy zucchini cookies? 
• We love making these corn and zucchini fritters in the summer. 
• Want to add nutrition to pizza night? Try this zucchini pizza crust!
• The simplest way to use zucchini is in this zucchini smoothie – it’s delicious! 

The links in this post are affiliate links, thank you for supporting JoyFoodSunshine.