Healthy Zucchini Muffins

This healthy zucchini muffin recipe yields moist, tender muffins using simple ingredients. I love how they bake in under 20 minutes.

Craving more healthy muffin recipes? Try my almond flour muffins, healthy pumpkin muffins, healthy blueberry muffins, and protein muffins next.

I’m always looking for an excuse to sneak zucchini into my favorite desserts, and muffins are my favorite. Contrary to skeptics, you really can’t taste it at all, yet it adds tons of moisture and sneaks in a fair share of vitamins and minerals. Bonus? My recipe has actually won a few awards, too!

Table of Contents

1. Why I love this recipe
2. Ingredients needed
3. How to make healthy zucchini muffins
4. Recipe tips and variations
5. Storage instructions
6. More zucchini dessert recipes to try
7. Healthy Zucchini Muffins (Recipe Card)

Why I love this recipe

• Perfect texture and flavor. Like my healthy zucchini bread, the muffins are soft and tender in the center, with melted chocolate in every bite. 
• Wholesome swaps. Whole wheat flour and simple baking staples make a muffin recipe I can feel good about sharing with family. 
• Easy to adjust. Without any extra effort, you can make these muffins gluten-free or dairy-free. 
• You can’t taste the zucchini. If I’m wrong, you can let me know in the comments. But until then, I stand by my statement!

Ingredients needed

• White Whole Wheat Flour. A healthier alternative to all-purpose flour, white whole wheat flour has added fiber and more whole grains. I’ve also tried this with gluten-free flour to keep it gluten-free.
• Coconut sugar. A refined sugar free sweetener, coconut palm sugar has no coconut taste, but a gorgeous dark color, similar to brown sugar. You can use any granulated sweetener of your choice.
• Baking powder and baking soda. Both leavening agents help the muffins rise and also remain fluffy.
• Cinnamon. Adds some delicious cinnamon flavor. I love using Saigon cinnamon, as it has a more pronounced cinnamon taste.
• Coconut oil OR olive oil. Both these oils are heart-healthy, and healthier oil alternatives to more traditional oils. If you don’t have either of them on hand, use any neutral-tasting oil.
• Yogurt of choice. Yogurt adds moisture to the muffins, keeping them moist inside, without the need for any butter. I like to use Greek yogurt for the extra protein, but any thick yogurt works.
• Milk. I typically use non-fat milk or almond milk. Use whatever you have on hand.
• Zucchini. Be sure to shred your zucchini finely, and remove excess moisture ONLY if it is super wet.
• Vanilla extract. I always add vanilla extract to my baked goods- it’s a non-negotiable.
• Chocolate Chips. Optional, but highly recommended.

How to make healthy zucchini muffins

I’ve included step-by-step photos below to make this recipe easy to follow at home. For the full printable recipe instructions and ingredient quantities, scroll to the recipe card at the bottom of this post.

Step 1- Mix wet and dry ingredients. In a mixing bowl, combine the dry ingredients. In a separate bowl, combine the wet ingredients. 

Step 2- Combine. Fold the dry ingredients into the wet ingredients until combined. Stir in the chocolate chips, then pour the batter into the muffin tins. 

Step 3- Bake the muffins for 15-17 minutes or until a toothpick comes out ‘just’ clean.

Recipe tips and variations

• Measure the zucchini before removing the excess moisture. Otherwise, you’ll add too much, and the texture will be off. 
• Make mini muffins. Pour the batter into mini muffin tins and bake for 10-12 minutes. 
• Swap the mix-ins. Instead of chocolate chips, fold in fresh or frozen blueberries, chopped nuts, or shredded coconut. 
• Enhance the flavor of the muffins. Fold in two tablespoons of orange zest, poppy seeds, or almond butter. 

Storage instructions

To store: Leftover muffins can be kept in an airtight container at room temperature for up to 3-4 days or in the refrigerator for up to 2 weeks. 

To freeze: Transfer leftover muffins to a freezer-safe container and freeze for up to 3 months. 

More zucchini dessert recipes to try

• Zucchini bars
• Zucchini pancakes
• Zucchini brownies
• Chocolate zucchini bread
• Zucchini chocolate cake
• Zucchini cookies

Originally published May 2020, updated and republished April 2024