Gluten Free Chocolate Zucchini Muffins
Why You’ll Love These Gluten Free Chocolate Zucchini Muffins
These Gluten Free Chocolate Zucchini Muffins are rich, moist and packed with deep chocolate flavour. Made with almond flour, these double chocolate zucchini muffins are naturally gluten-free, grain-free and low in carbs, making them a delicious option for breakfast, snacks or healthy desserts. And in my opinion, they qualify to be in the “protein muffins” category, just like my Triple Chocolate GF Banana Protein Muffins, since each muffin has 6 grams of protein. Every bit counts when we’re reaching for that daily goal!
The zucchini keeps these healthy gluten free muffins incredibly soft and moist while adding extra moisture without an overpowering zucchini taste. Even picky eaters will love them! In fact, my husband said these words after trying them: “these are amazing.” And I have to say, I agree!
Like my GF Zucchini Chia Muffins, these gluten free zucchini chocolate chip muffins are also perfect for meal prep. They come together in just one bowl with about 10 minutes of prep time, making them an easy grab-and-go option for busy mornings, road trips or afternoon snacks. And, the fact that they’re low-sugar means you can have as many as you want, really! Whether you’re looking for healthy chocolate zucchini muffins or an easy way to use up fresh zucchini, this recipe is sure to become a favourite of yours.

Recipe Notes and Ingredients Tips
Here’s a few things to keep in mind:
- Almond flour – Almond flour is naturally gluten-free, grain-free and low carb. You can buy it at most grocery stores. Be sure to get almond flour and not almond meal. Almond meal contains the skins of the almonds so it makes for a grittier texture.
- Cocoa powder – Using dutch-processed cocoa powder is what gives these muffins that deep, dark, rich brown colour. Regular cocoa powder works too.
- Xylitol – xylitol is great for baking because it’s low-carb, sugar-free and it tastes just like sugar! No weird aftertaste. Regular granulated sugar works too .
- Yogurt – Adding a little plain yogurt helps the muffins to rise as it activates the baking soda. It helps to keep these muffins moist too! You will need plain greek yogurt for this recipe.
- Zucchini – It will take about 1 medium-large sized zucchini to get 2 cups of shredded zucchini. The 2 cups is measured out after the zucchini has been squeezed.
How to Make Gluten Free Chocolate Zucchini Muffins
Step 1: Mix the wet ingredients.
Preheat the oven to 350F and line 2 muffin trays with 14 muffin liners. I prefer to space them out and do 7 liners in each tray. In a medium-sized bowl, beat the softened butter and xylitol together until smooth and combined. Add the eggs, one by one until combined. Then, add the yogurt and vanilla and mix again.

Step 2: Add the dry ingredients.
To the same mixing bowl with the wet ingredients, add the almond flour, cocoa powder, baking powder, baking soda and salt. Whisk until the dry ingredients are completely combined with the wet ingredients and there are no dry pockets. Fold in the chocolate chips.

Step 3: Add the shredded zucchini.
Add the shredded zucchini to a dark-coloured dish towel and, over the sink, squeeze as much excess liquid out as possible. You can also just use your hands and do it in batches. Measure out 2 cups shredded zucchini after it’s been squeezed and then add it to the mixing bowl with the muffin batter in it. Fold into the batter.

Step 4: Transfer muffin batter to liners and bake!
Spoon the chocolate zucchini muffin batter evenly into the 14 paper liners and bake in the preheated oven for 19-21 minutes. Check them with a toothpick at 19 minutes, so not to over bake them. Let cool 15 minutes and enjoy!


Expert Tips for Healthy Chocolate Zucchini Muffins
- Use a dish cloth or towel to squeeze out as much liquid from the zucchini as you can before adding it to the mix. If the liquid is not squeezed, you will end up with a very sloppy, wet muffin.
- You don’t have to mix the wet and dry ingredients separately; just use one bowl – less mess!
- If you really want to bring out the chocolate flavour, try adding 1 tsp of espresso powder or super fine coffee grounds. This will really make the chocolate pop.
- Dutch-processed cocoa powder isn’t required, but it does give the muffins that beautiful, deep, dark brown colour.
FAQ
No, you can’t taste the zucchini in these muffins. While the shredded zucchini does add texture and you can see that it’s there, any flavour is masked by the delicious flavours of chocolate!
No. There’s no need to peel the zucchini before shredding it. The peel softens while baking and blends seamlessly into the muffins. Do wash it well first though!
The shredded zucchini adds natural moisture to the muffins, helping keep them soft and tender. Greek yogurt also helps create a moist texture in gluten free baking.
Yes! These gluten free chocolate zucchini muffins freeze very well. Store them in an airtight container or freezer-safe bag for up to 3 months. To store in the fridge, keep them in an air tight container for up to 5 days. Eat them cold or heat in the microwave for 15-20 seconds. I actually love them cold!
These healthy chocolate zucchini muffins are made with almond flour and shredded zucchini, making them naturally gluten-free and grain-free. They’re also sugar-free and low-carb by using xylitol as the main sweetener. They’re a great healthy option for breakfast, snacks or meal prep.

GF Double Chocolate Zucchini Muffins
Equipment
- 2 Muffin Tins
Ingredients
- 1/4 cup unsalted butter softened to room temperature
- 2/3 cup non-GMO xylitol or regular sugar
- 4 eggs at room temperature
- 1/4 cup plain greek yogurt
- 1 teaspoon pure vanilla extract
- 2 cups almond flour
- 1/3 cup dutch-processed cocoa powder
- 1 1/2 teaspoons baking powder
- 1/2 teaspoon baking soda
- 1/4 teaspoon sea salt
- 2 cups shredded zucchini squeezed and lightly packed
- 1/2 cup chocolate chips plus more for topping
Instructions
- Preheat the oven 350F and line two muffin tins with 14 paper liners, 7 in each one. Set aside.
- In a medium-sized bowl, whisk together the softened butter and xylitol until combined. Add the eggs one at a time, mixing in between. Then add the yogurt and vanilla and whisk again until combined.
- Add the almond flour, cocoa powder, baking powder, baking soda and salt and whisk until fully combined.
- Fold in the chocolate chips.
- Add the shredded zucchini to a dish towel and squeeze out as much liquid as possible. Measure out 2 cups of shredded zucchini, lightly packed. Then, fold it into the muffin batter until combined.
- Scoop the batter into the prepared muffin liners until you have 14 equally filled cups. Top with extra chocolate chips if desired.
- Bake in the preheated oven for 19-21 minutes or until a toothpick inserted comes out clean. Check at 19 minutes. You don't wan't to over-bake them.
- Let cool for at least 15 minutes and then enjoy!
Notes
- Almond flour – You can buy it at most grocery stores these days. Be sure to get almond flour and not almond meal.
- Cocoa powder – Using dutch-processed cocoa powder is what gives these muffins that deep, dark, rich brown colour. Regular cocoa powder works too.
- Xylitol – I love using xylitol for baking because it’s low-carb, sugar-free and tastes just like sugar! No weird aftertaste. You can use regular granulated sugar in this recipe too if you aren’t low-carb.
- Zucchini – It will take about 1 medium-large sized zucchini to get 2 cups of shredded zucchini. The 2 cups is measured out after the zucchini has been squeezed.