Wondering what to do with extra zucchini? Full of chocolate flavour and studded with chocolate chips, these Gluten-Free Double Chocolate Zucchini Muffins are a great way to use summer squash! Made with a gluten-free flour blend, coconut sugar and Greek yogurt, these muffins are moist and tender and insanely delicious.

Zucchini season is upon us in full force. If you're searching for ways to use it up, see 8 Delicious Zucchini Recipes Ideas. But wait: What better way could there be to enjoy zucchini than with a Gluten-Free Double Chocolate Zucchini Muffin? Or two!
I love the texture zucchini gives baked goods. While it keeps them moist and tender, it doesn't impart any strong zucchini flavour. It simply, and very kindly, contributes all its nutritious benefits to a lowly muffin!
I make these grain-free Zucchini Banana Muffins and Double Chocolate Zucchini Bread often during zucchini season, but today, chocolate muffins won!
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🛒 Ingredients
Gather your ingredients! Here's what you'll need to make this super moist chocolate zucchini muffins.
- gluten-free all-purpose flour mix: I like Bob's Red Mill 1 to 1 Gluten-free Baking Mix or Cup 4 Cup Gluten-free Baking Mix
- salt
- baking soda
- cocoa powder: one of the chocolates in double chocolate!
- granulated sugar
- coconut sugar or brown sugar: give lots of caramel flavour and a slight chewy texture
- eggs: for a boost of protein
- light oil or light olive oil
- vanilla extract
- Greek yogurt: or you can use a plant-based yogurt to keep this recipe dairy-free
- zucchini: very well-drained. Zucchini adds lots of moisture to these muffins, so shred it up and squeeze out as much extra moisture as you can.
- chocolate chips: dairy-free if necessary
👍🏼Helpful tips
- I used Bob's Red Mill Gluten-Free 1-to-1 Baking Flour in this recipe. I've tried many gluten-free flour blends in the past, but I have had the most success with this one. It contains xanthan gum, so you don't need to add it yourself.
- I lowered the sugar content a little by using half coconut sugar (with a lower glycemic index) and half granulated sugar.
- Adding a little Greek yogurt to the batter along with baking soda helps the muffins to rise. It also improves the texture. (Use coconut yogurt for a dairy-free muffin.)
- Throughly drain the grated zucchini by squeezing it in cheesecloth or a clean tea towel. Removing the excess water will prevent the muffins from being soggy.
- Stir the chocolate chips into the batter. Save a few to press into the top of the muffins before baking.
🔪 Instructions
These Gluten-Free Double Chocolate Zucchini Muffins are easy to bake.
Follow a standard muffin method for success every time. Whisk the dry ingredients, mix the wet ingredients, add the shredded, drained zucchini and yogurt and stir until just combined. Gently fold in the chocolate chips, saving a few to press into the top of each muffin.
Bake, cool slightly and add a slather of butter, if you like!
🥶How to store and freeze muffins
These gluten-free muffins will stay fresh in a container on the counter for a day or two. For longer storage, keep them covered in the fridge.
These muffins freeze well when you wrap them individually or when stored in a covered container lined with a paper towel. They will last in the freezer for up to 3 months.
🗒 More gluten-free muffin recipes!
📖 Recipe
Gluten-Free Double Chocolate Zucchini Muffins
Ingredients
- 2 cups gluten-free all purpose flour mix
- 1 ⅕ teaspoon xanthan gum * only use if your GF flour mix doesn't contain xanthan gum or guar gum
- ½ teaspoon salt
- 1 ½ teaspoon baking soda
- ½ cup cocoa powder
- ½ cup granulated sugar
- ¼ cup coconut sugar or brown sugar
- 2 large eggs
- ½ cup light oil or light olive oil
- 1 teaspoon pure vanilla extract
- ½ cup Greek yogurt
- 3 cups grated zucchini, drained* see note below
- ¾ cup chocolate chips* save some to press into muffin tops before baking. Use dairy-free if necessary.
Instructions
- Preheat oven to 350°F. Line two 12-cup muffin tins with culinary paper liners.
- Whisk gluten-free flour, xanthan gum (if using), salt, baking soda and cocoa in a medium bowl.
- Mix oil, both sugars, eggs, and vanilla in a large bowl or in the bowl or in the bowl of a stand mixer. Beat until fluffy. Gently stir in yogurt and grated and drained zucchini. Stir dry ingredients into batter just until combined.
- Fold in chocolate chips, saving some to press into the tops of the muffins before baking.
- Fill muffin cups ¾ full. Bake at 350°F for 18 - 20 minutes or until toothpick inserted comes out clean. Cool 10 minutes, then transfer to wire rack and remove paper liners.
Notes
Nutrition
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Clara
Can I use buttermilk instead of yogurt if I don't have any yogurt? Or sour cream maybe?
Elaine
Hi Clara, Sour cream would be a good substitute for yogurt.
Crystal
Amazing! My kids loved them. Better than chocolate cake
Flavour & Savour
That's great news! Thanks for taking the time to let me know!
Dierdre
My son loves these muffins! I think it's a great way to add some vegetables into a sweet treat. He likes all those chocolate chips on top, too!
Flavour & Savour
We love these too! Lots of chocolate, but healthy zucchini too! Thanks for letting me know!