Healthy Food Recipeub July 12, 2026 0 Comments

Chocolate Zucchini Muffins – (The Best Recipe + Video)

These homemade chocolate zucchini muffins are loaded with rich chocolate flavor. They’re healthy enough for breakfast and decadent enough for dessert!

Why you’ll love these chocolate zucchini muffins

Soft, moist texture. The hidden vegetable adds moisture without extra fat, giving you perfectly fluffy muffins every single time.
Two types of chocolate. Using both high quality cocoa powder and chocolate chips makes these double chocolate muffins extra chocolatey and delicious.
Family favorite muffins. I’ve been baking this recipe for years, and my entire family loves it too. The cake-like chocolate muffins are a great way to use up farmers market zucchini or sneak more veggies into your diet. No one can ever tell!
Dairy free & low calorie. They’re under 100 calories each, with egg free, gluten free, vegan, and sugar free options. Thanks to the zucchini and antioxidant rich cocoa, each muffin offers health benefits, including 14% of the RDA for fiber and 7% iron.
Easy to make, easy to eat. You need just one bowl and a few basic ingredients. The recipe is freezer friendly and non messy. It’s a good choice for any time you want an instant breakfast or a quick snack on the go.

You may also love this Healthy Chocolate Banana Bread

Step by step recipe video

Healthy Zucchini Muffin Ingredients With Chocolate Chips

Key ingredients

Zucchini – The recipe calls for three fourths of a cup grated fresh zucchini, which equals about one medium green zucchini. Feel free to substitute an equal amount of yellow summer squash.

Cocoa Powder – Use unsweetened cocoa powder as opposed to Dutch processed cocoa. It should be readily available in the baking aisle of most grocery stores. You may sub chocolate protein powder for up to two tablespoons of the cocoa if preferred.

Flour – I’ve had success with all purpose white flour, cup for cup gluten free flour, and spelt flour. The spelt is my personal favorite, because it’s whole grain and yields a lighter cake texture than using whole wheat flour.

*For those interested in a keto or paleo zucchini recipe, try this Almond Flour Zucchini Bread.

Sweetener – This can be classic white sugar, unrefined cane sugar, or any sugar free granulated sweetener that measures like sugar. I’ve not tried pure maple syrup or honey here so cannot vouch for liquid sweeteners as a substitution.

Vanilla Extract – Pure vanilla extract enhances the deep chocolate flavor in the muffins. For the best taste, buy pure vanilla extract instead of imitation.

Water – I like making a vegan version of the recipe, which still rises just fine without eggs. If you are not plant based, you can swap out the water for two whole eggs.

Other Ingredients – Salt adds depth of flavor, and baking powder acts as a leavening agent, giving the finished muffins a nice domed top.

Oil (optional) – The cupcakes will taste richer with a tender crumb if you include a fourth cup of vegetable oil or melted coconut oil. Unsalted butter or nondairy butter also works.

For oil free and low fat healthy chocolate zucchini muffins, replace the oil with high protein Greek yogurt or mashed banana. Chocolate banana zucchini bread muffins? Yes, please.

Chocolate Chips (optional) – As a chocoholic, I almost always stir a generous handful of mini dark chocolate chips into the batter and sprinkle some more on top. You can never have too much chocolate!

How to make the recipe

Begin by preheating the oven to 350° Fahrenheit or 176° Celsius. Line or grease a standard size cupcake pan, or take out a silicone muffin pan.
Wash and finely grate the zucchini, using a box grater or a food processor. Set the grated zucchini aside.
Next, combine the dry ingredients (flour, cocoa powder, sweetener, baking powder, salt, and optional chocolate chips) in a large mixing bowl. Stir until well mixed.
Whisk the wet ingredients (zucchini, oil or yogurt, eggs or water, and pure vanilla extract) into the bowl of dry ingredients until just evenly mixed. Do not over-stir.
Portion the chocolate muffin batter into your prepared baking pan. It should fill up a dozen muffin tins about two thirds of the way.
Add more chocolate chips to the tops if desired. Then bake on the center rack of the oven for sixteen minutes or until muffins have risen. A toothpick inserted into the center of a muffin should come out mostly clean when they are done.
Let the chocolate baked goods cool before enjoying plain, or spread with peanut butter, almond butter, cream cheese, or any other garnishes of choice.

Katie’s tips for the best chocolate zucchini muffins

Start with quality ingredients. Look for firm zucchini without any soft spots or wrinkles. Choose a thinner vegetable, because super thick summer squashes often contain excess water. And high quality cocoa powder will give you the most decadent chocolate taste.

Follow the recipe. Follow the instructions exactly the first time you make these muffins, without changing or omitting any ingredients. Once you see how the recipe should turn out, have fun customizing it with different flours, sweeteners, etc.

Calibrate your oven. Many ovens are not properly calibrated, which can cause uneven results when baking. If the oven is set to 350 degrees, an oven thermometer should also read 350 degrees.

Let cool. Allow muffins to cool fully before transferring to a container. Store on the counter overnight, loosely covered in a towel. Any leftovers after a day should be refrigerated in a covered container for up to four days. Or freeze for up to three months, and thaw frozen muffins before consuming.

Want to turn this into a mini muffin recipe? Use the recipe below, using mini muffin pans. The mini chocolate zucchini muffins should take around eight minutes to bake.

Or make chocolate zucchini cupcakes. Just top with Chocolate Cream Cheese Frosting or your favorite store bought or homemade icing.

The recipe was adapted from my Chocolate Zucchini Cake and this Chocolate Zucchini Bread.

1. Preheat the oven to 350° Fahrenheit (176° Celsius). Line or grease a standard size muffin tin.
2. Add the flour, cocoa powder, sweetener, baking powder, salt, and chocolate chips to a large bowl and stir very well.
3. Whisk in the wet ingredients (zucchini, eggs or water, oil, and vanilla extract) until just evenly mixed. Do not over-stir the batter.
4. Divide the mixture evenly into the muffin tin. Sprinkle more chocolate chips on top if you wish.
5. Bake on the oven’s center rack for 16 minutes or until a toothpick inserted into the center comes out mostly clean.
6. Let cool, then enjoy. If you can wait, the chocolate zucchini muffins taste even more delicious the next day!
7. Once cooled, store leftovers loosely covered at room temperature overnight or in a covered container in the refrigerator or freezer for longer storage.