These healthy chocolate zucchini muffins are made with Greek yogurt, whole wheat pastry flour, and less sugar than traditional muffins. They're incredibly moist thanks to shredded zucchini and get a double dose of chocolate from cocoa powder and chocolate chips.


Notes from my kitchen
I used my tried-and-true muffin template to create a zucchini muffin for chocolate lovers.
I consider it the summer alternative to my healthy chocolate pumpkin muffins and a chocolatized version of my Greek yogurt zucchini muffins.
Not only are they packed with veggies, but they get a protein boost from Greek yogurt. That's enough virtue for me to happily serve them for breakfast or as a healthy snack.
By the way, you can't taste the zucchini. My favorite part is watching someone enjoy a chocolate muffin with hidden zucchini before they discover the secret ingredient. 😉
Marjory
Ingredients

Of special note:
- Zucchini - Grated zucchini keeps the muffins moist without adding any noticeable flavor.
- Flour - Use whole wheat pastry flour or white whole wheat flour for a soft, tender muffin. All-purpose flour, or a combination with whole wheat flour, will also work.
- Sugar blend - I used a 50/50 blend of sugar and a sugar alternative to reduce sugar and carbs. You can buy a blend like this or mix your own. If you prefer, use regular granulated sugar.
- Greek yogurt - Greek yogurt replaces much of the fat while adding moisture and protein. I used nonfat Greek yogurt, but low-fat or whole milk Greek yogurt can be used instead.
- Chocolate - I've used all types of chocolate chips in this recipe. I prefer mini ones because they distribute nicely. Stevia-sweetened ones keep the carb count down. You can also chop a bar of your favorite dark chocolate.
The recipe card below includes ingredient amounts, step-by-step instructions, and nutritional information.
Extra zucchini shreds?
Make zucchini blueberry muffins or freeze the extra shredded zucchini for another batch.
How to Make Healthy Chocolate Zucchini Muffins
Shred zucchini

Shred zucchini with a box grater or food processor and press out excess moisture. Measure 2 cups of shreds for the muffins and reserve the remainder for another recipe.
Mix ingredients

Combine flour, sugar blend, baking powder, baking soda, salt, cinnamon, and cocoa powder in a bowl. Next, add a beaten egg, vanilla extract, and Greek yogurt to the dry ingredients and stir to combine. The batter is stiff at this stage, and that is normal.
Add zucchini

Add the zucchini shreds and continue stirring until the batter softens. It will still be thick. Add a little milk, if necessary, until it is the consistency of a thick dip. Fold in the chocolate chips.
Fill muffin cups

Place muffin liners in a muffin tin and spritz with non-stick cooking spray. Since this recipe has no oil, this step is necessary to prevent sticking. Fill each muffin cup about two-thirds full. Don't overfill, as the tops may spill over while they bake and not hold a domed form.
Bake

Bake for 20-25 minutes or until the muffins are firm. Don't overcook.
Make a Half Batch
This recipe is easily halved if you'd like to make a smaller batch or try it before committing to a full batch.
Breakfast idea with healthy chocolate zucchini muffins
I like to pair these healthy chocolate zucchini muffins with chia seed pudding made with yogurt or zucchini egg muffins. These recipes share ingredients and you can prepare them all ahead of time for quick and easy breakfasts all week long.
Would you like more easy, healthy, carb-conscious recipes?
📋 Recipe

Healthy Chocolate Zucchini Muffins
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Ingredients
- 2 cups shredded zucchini 2 large zucchini
- 1½ cups whole wheat pastry flour white whole wheat or unbleached all-purpose flour
- ⅔ cup Sugar blend or granulated sugar to equal ⅔ cup
- ½ teaspoon baking powder
- ½ teaspoon baking soda
- ½ teaspoon salt
- 1 teaspoon ground cinnamon
- ¼ cup cocoa powder
- 2 large eggs
- 1 Tablespoon milk any kind as needed to thin batter
- ½ cup Greek yogurt, nonfat or whole milk
- ½ cup chocolate chips preferably mini size and stevia-sweetened, any type will work
Instructions
- Preheat oven to 375℉.
- Shred zucchini with a box grater or food processor and press out excess moisture. Measure 2 cups of shreds for the muffins and reserve the remainder for another recipe.
- Combine flour, sugar blend, baking powder, baking soda, salt, cinnamon, and cocoa powder in a bowl. Add eggs and Greek yogurt and stir to combine. The batter should be very stiff at this point.
- Add shredded zucchini and continue stirring. As the zucchini is incorporated into the batter, it will become softer, but will still be quite thick. Add a little milk, 1 teaspoon at a time, if necessary, until the batter is the consistency of a thick dip.
- Fold in chocolate chips.
- Fill muffin tins coated with cooking spray about ⅔ full. (If using paper liners, give them a spritz too!) Don't overfill, as the batter will spill over the top of the muffin while it bakes.
- Bake for 20-25 minutes or just until the muffins are firm on top. Don't overbake.
- Allow muffins to cool for 5 minutes in the pan and then remove to a wire rack to cool further.
Notes
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Sania says
Awesome!!! I just tried this recipe and the muffins turned out yummy....My first try on Zucchini muffins and I feel so happy.. Thank You.
Hayley says
These are delicious! Even my super picky 6 yo ate a bunch. I made mini muffins, they still cooked for 20 min. I would double, or triple the recipe next time. Thanks!
Marjory Pilley says
I'm so glad you enjoyed them and thanks so much for commenting with the mini-muffin time! They freeze well too!
Joni says
This sounds delicious and I plan on trying it. But one question, do you remove the seeds of the zucchini before grating it?
Marjory Pilley says
Hi! You do not need to remove the seeds!
Tara says
Yum! I love the moisture the zucchini adds to these muffins. Such a great use for the veggie and an excuse to eat chocolate!