Chocolate Chip Zucchini Muffin in Silcone liner next to muffin tin

Skinny Double Chocolate Zucchini Muffins

An easy recipe for low fat, whole grain, protein packed, Healthy Chocolate Zucchini Muffins. 
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Course: Bread
Cuisine: American
Keyword: Chocolate Zucchini Muffins, Zucchini Muffins
Prep Time: 10 minutes
Cook Time: 20 minutes
Total Time: 30 minutes
Servings: 20
Calories: 98kcal
Author: Kristen Chidsey


  • 2 cups white wheat flour
  • 1 teaspoon baking soda
  • 1 teaspoon baking powder
  • 1/4 teaspoon salt
  • 1/2 cup cocoa powder
  • 2/3 cup maple syrup
  • 1/2 cup plain Greek yogurt
  • 2/3 cup milk
  • 1/4 cup applesauce
  • 1 egg
  • 1 teaspoon vanilla extract
  • 1 1/2 cups zucchini shredded, and squeezed dry
  • 1/3 cup chocolate chips optional


  • Preheat oven to 350 degrees. Prepare muffin tin by lining with silicone liners, paper liners, or greasing well. 
  • Shred zucchini and place in colander and press down hard or squeeze excess liquid out of zucchini by placing zucchini in cheesecloth or a clean kitchen towel and squeezing firmly.
  • In a large mixing bowl, mix together flour, cocoa powder, baking powder, baking soda, and salt, until well combined. It is an even better idea to sift the dry ingredients together to remove any lumps from flour or cocoa powder.
  • Mix zucchini into the dry ingredients, mixing to evenly distribute zucchini throughout dry ingredients. 
  • In a separate mixing bowl, whisk together milk, yogurt, egg, applesauce and vanilla extract until well combined. 
  • Add wet ingredients to dry ingredients and stir until just combined, careful to not over mix. 
  • Scoop out 1/4 cup batter into prepared muffin tin. Sprinkle each muffin with a couple chocolate chips.
  • Bake for 18-20 minutes, or until toothpick inserted in middle comes out dry. 


  • You can use any type of milk you like for these chocolate zucchini muffins. 
  • Be sure to use plain Greek yogurt to keep these zucchini muffins refined sugar free. 
  • In place of the applesauce, you can use 1/4 cup melted coconut oil or canola oil. 
  • I use whole white wheat flour to keep these muffins full of whole grains, yet light and fluffy. You can substitute all-purpose or whole wheat flour for the whole white wheat flour in this recipe. 
  • If you are looking for Gluten-Free Chocolate Zucchini Muffins, use an all-purpose gluten-free 1 to 1 baking flour. 
Nutrition Facts
Skinny Double Chocolate Zucchini Muffins
Amount Per Serving
Calories 98 Calories from Fat 9
% Daily Value*
Total Fat 1g 2%
Sodium 93mg 4%
Potassium 144mg 4%
Total Carbohydrates 20g 7%
Dietary Fiber 2g 8%
Sugars 9g
Protein 3g 6%
Vitamin A 1%
Vitamin C 2.7%
Calcium 5.2%
Iron 3.8%
* Percent Daily Values are based on a 2000 calorie diet.