Chocolate Chip Zucchini Muffins

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Sometimes muffins can be a little too close to cake. While I know we all want that tender moist crumb when we take the time to bake them from scratch, but there’s no need to overdo it. That’s because it is so easy to do a few swaps when you make these healthy chocolate chip zucchini muffins. You won’t miss the sugar or the other usual ingredients.

Three chocolate chip zucchini muffins on a plate with one torn in half.

What Makes These Muffins Healthy

Whole wheat pastry flour takes the place of all-purpose flour. It’s a simple way to add whole grains to this zucchini muffin recipe without sacrificing that soft, fluffy consistency.

Instead of sugar, the muffins are sweetened with maple syrup, which has a lower glycemic level than refined sugar. Again, I don’t think muffins should ever be as sweet as cupcakes.

Greek yogurt adds its signature tang and taste, and it makes the muffins moist. It’s a lighter option for baked goods than butter or sour cream.

The Ingredients

Ingredients including flour, shredded zucchini, eggs, vanilla extract, yogurt and spices.

This is what you need:

  • Whole wheat pastry flour is milled from soft white wheat unlike whole wheat flour which is milled from red hard wheat. I like pastry flour for muffins because you end up with a softer, finer texture. You can substitute and use all-purpose flour, but you will miss out on the whole grains.
  • Baking powder & baking soda are both necessary to help the muffins rise as they bake in the oven.
  • Spices: As mentioned, I take my beloved homemade chai concentrate for inspiration and include a mix of cinnamon, ginger, cardamom, nutmeg and cloves. Because these muffins don’t use granulated sugar, they aren’t overly sweet. I like to boost the flavor by going all in on dried spices.
  • Coconut oil is the fat in the recipe that adds a hint of flavor and moisture to the muffins. Overall the coconut is not strong.
  • Maple syrup sweetens the muffins instead of white sugar.
  • Eggs: The recipe calls for 2 large eggs beaten into the wet ingredients.
  • Vanilla extract gives the muffins a little bit of vanilla flavor.
  • Greek yogurt: Either use 2% of whole milk yogurt for the recipe.
  • Zucchini that’s fresh and firm and has no soft spots is the best for shredding.
  • Mini chocolate chips give the muffins sweet, slightly indulgent chocolate flavor.

Optional Additions & Substitutions

You don’t have to include chocolate chips in these zucchini muffins. Skip the chips or try another mix-in:

  • Nuts such as chopped walnuts or pecans
  • Dried fruit such as cranberries or blueberries

How To Make These Chocolate Chip Zucchini Muffins

Preheat the oven to 400 degrees F. Line a 12-cup muffin pan with paper liners.

1. Combine the dry ingredients in a large mixing bowl. That includes the whole wheat pastry flour, baking powder, baking soda, cinnamon, ginger, cardamom, nutmeg, cloves and salt.

2. Whisk together the coconut oil, maple syrup, eggs and vanilla extract in another bowl.

Combine the dry ingredients in a bowl. Whisk the wet ingredients in another bowl.

3. Fold the wet ingredients into the flour mixture. Use a big spoon or a spatula to stir slowly until most of the dry ingredients have been mixed in.

4. Stir in the grated zucchini, Greek yogurt and chocolate chips. Do not over mix.

5. Spoon the batter into the muffin tin and top with additional chocolate chips.

6. Bake the muffins until they are golden, about 17-19 minutes. To know if they are ready, you can poke them with a toothpick to see if it comes out clean. Also, the muffins should spring back when you softly press the tops of them.

7. Cool the muffins in the pan for 10 minutes before removing them. Then let them cool on a wire rack.

Spoon the batter into the muffin pan and top with chocolate chips; baked muffins in the pan.

Recipe Tips

Use the large holes of a box grater or the shredding disk on a food processor to shred the zucchini. Then make sure to squeeze or press out as much water as you can from the zucchini using a towel. If it’s too wet, you will end up with dense muffins.

You don’t need to peel the zucchini before you shred it. The skin is thin and bakes right into the muffins. Also, you want to see those green flecks running through the muffins.

Make sure the maple syrup, eggs and yogurt are at room temperature before you whisk them with the melted coconut oil. This will prevent the coconut oil from solidifying again.

Don’t over mix the batter. Slowly and gently fold the wet ingredients into the dry ingredients. Stop stirring the moment when you no longer see any flour. 


You can eat the muffins warm or at room temperature. They are best the day they are baked, but you can revive them in a 350-degree oven for a 3-5 minutes. When the muffins are warm, they will be a little messier to eat because the chocolate chips will be melted to the touch.

Storage & Freezing

Leftover muffins can be stored in an airtight container at room temperature up to 3 days. Do not put them in the fridge. To keep them longer, store them in the freezer up to 1 month and thaw them at room temperature.

Nine zucchini muffins on a wire rack.

More Muffin Recipes

Vegan Apple Cinnamon Muffins
Vegan Blueberry Chia Muffins

Let me know if you if you baked these muffins. Please leave a comment and rating below. Thanks!

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Chocolate Chip Zucchini Muffins

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Prep: 10 minutes
Cook: 18 minutes
Total: 28 minutes
Servings: 12 muffins
Sweetened with maple syrup and made with Greek yogurt, these lighter zucchini muffins with chocolate chips have a chai-inspired blend of spices including cinnamon, ginger and cardamom.


  • 2 cups whole wheat pastry flour
  • 1 teaspoon baking powder
  • 1/2 teaspoon baking soda
  • 1-1/2 teaspoons ground cinnamon
  • 1 teaspoon ground ginger
  • 1/4 teaspoon ground cardamom
  • 1/8 teaspoon ground nutmeg
  • 1/8 teaspoon ground cloves
  • 1/2 teaspoon kosher salt
  • 1/3 cup melted coconut oil
  • 1/2 cup maple syrup
  • 2 large eggs
  • 1 teaspoon vanilla extract
  • 1/2 cup Greek yogurt
  • 1-1/2 cups shredded zucchini (about 2 medium zucchini), excess water squeezed out
  • 1/2 cup mini chocolate chips plus more for muffin tops


  • Preheat the oven to 400 degrees F. Line a 12-cup muffin pan with paper liners.
  • In a large bowl, combine the flour, baking powder, baking soda, cinnamon, ginger, cardamom, nutmeg, cloves and salt.
  • In a medium bowl, whisk together the coconut oil, maple syrup, eggs and vanilla extract.
  • Fold the wet ingredients into the dry ingredients. When they are almost combined, add the yogurt, zucchini and chocolate chips. Gently stir everything together. Be careful not to over mix the batter.
  • Spoon the batter into the muffin cups. Top with additional chocolate chips.
  • Bake for 17-19 minutes until the muffins are golden and a toothpick inserted in the center comes out clean.
  • Cool on a wire rack for 10 minutes. Then remove the muffins and let them finish cooling on the rack.


Make sure your eggs and yogurt are at room temperature before mixing them with the rest of the wet ingredients.
You can leave out the chocolate chips or add chopped nuts or dried fruit instead.
Store leftover muffins in an airtight container at room temperature up to 3 days. You can freeze them up to 1 month. Thaw at room temperature.


Calories: 218kcal | Carbohydrates: 30g | Protein: 5g | Fat: 9g | Saturated Fat: 7g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 1g | Trans Fat: 0.02g | Cholesterol: 29mg | Sodium: 201mg | Potassium: 195mg | Fiber: 3g | Sugar: 14g | Vitamin A: 124IU | Vitamin C: 5mg | Calcium: 73mg | Iron: 1mg

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

Additional Info

Course: Quick Breads & Muffins
Cuisine: American
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Hi, I'm Paige.

Welcome to Last Ingredient where you will find simple seasonal recipes with plenty of fruits and vegetables, all for the home cook.

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