Get ready for a muffin that’s secretly healthy but tastes like a decadent, fudgy brownie! These Gluten Free Chocolate Zucchini Muffins are unbelievably moist, rich, and packed with double the chocolatey goodness. Using almond flour keeps them naturally grain-free, and the hidden zucchini adds incredible moisture without a trace of vegetable flavor.
Table of Contents

A Little Story About This Dish
My favorite challenge in the kitchen is creating a treat that’s both delicious and secretly nutritious. These muffins are my greatest success story! I first baked them as a way to use up the summer zucchini overflowing from my garden. When my family devoured the entire batch in one afternoon without ever suspecting they were packed with vegetables, I knew I had a winning recipe. These have become our go-to for a healthier, satisfying chocolate fix.
Get Ready to Cook!
What to Expect
These Gluten Free Chocolate Zucchini Muffins are incredibly simple to whip up. You’ll only need a couple of bowls and about 10 minutes of prep time. They bake in around 20 minutes, filling your kitchen with an amazing chocolate aroma. The result is a batch of super moist, tender muffins that taste more like a dessert than a healthy snack.
Before You Begin
The most important tip for perfect Gluten Free Chocolate Zucchini Muffins is to squeeze the shredded zucchini! Zucchini holds a lot of water, and removing the excess moisture is critical. Simply wrap the shredded zucchini in a paper towel or a clean kitchen towel and squeeze firmly. This step prevents the muffins from becoming too wet or dense and ensures a perfect, fudgy texture.
The Heart of the Dish: Ingredients You’ll Need
This recipe uses nutrient-dense almond flour and natural sweeteners to create a truly delicious batch of Gluten Free Chocolate Zucchini Muffins.
| Ingredient | Amount |
| Almond Flour | 2 cups |
| Unsweetened Cocoa Powder | 1/3 cup |
| Baking Soda | 1/2 tsp |
| Salt | 1/4 tsp |
| Eggs | 3 |
| Coconut Oil | 1/4 cup, melted |
| Maple Syrup | 1/3 cup |
| Vanilla Extract | 1 tsp |
| Finely Shredded Zucchini | 1 cup, squeezed dry |
| Chocolate Chips | 1 cup |
Let’s Get Cooking! Step-by-Step Guide
1. Prepare Your Oven and Muffin Tin
First, preheat your oven to 350°F. Prepare a standard 12-cup muffin tin by lining it with cupcake liners or giving each cup a thorough coat of non-stick spray to ensure your Gluten Free Chocolate Zucchini Muffins don’t stick.
2. Combine the Dry Ingredients
In a small bowl, whisk together the almond flour, cocoa powder, baking soda, and salt. Mixing these dry ingredients separately first helps ensure the leavening is evenly distributed, which leads to a perfect rise. Set this bowl aside for a moment.
3. Whisk the Wet Ingredients
Now, in a separate large bowl, whisk your three eggs. Add the melted coconut oil, pure maple syrup, and vanilla extract. Stir everything together until the mixture is smooth and well combined.
4. Mix the Batter
Pour the dry ingredient mixture into the large bowl containing the wet ingredients. Stir gently until the batter is just combined. Be careful not to overmix at this stage.

5. Fold in Zucchini and Chocolate
It’s time for the star ingredients! Gently fold your squeezed, dry shredded zucchini into the batter. Once it’s incorporated, stir in half of the chocolate chips. Saving the other half for the topping guarantees every muffin has a beautiful, chocolatey top.
6. Fill and Bake Your Muffins
Spoon the batter into your prepared muffin tin, filling each liner about three-quarters of the way full. Sprinkle the remaining chocolate chips evenly over the top of each muffin. Bake for 19 to 21 minutes. The best Gluten Free Chocolate Zucchini Muffins are ready when a toothpick inserted into the center comes out clean. Let them cool for a few minutes in the pan before transferring to a wire rack.

Mastering the Dish: Pointers for Perfection & How to Store
Don’t Skimp on the Chocolate: Using chocolate chips both inside the batter and sprinkled on top is the key to making these muffins extra decadent. As they bake, the chips on top create a beautiful, slightly crispy cap that everyone loves.
Let Them Cool: Allow the muffins to cool in the tin for at least 5-10 minutes before moving them. Almond flour baked goods are delicate when hot, and this cooling time helps them set up properly.
Storage: Proper storage is key for these Gluten Free Chocolate Zucchini Muffins. Once completely cooled, store them in an airtight container at room temperature for up to 3 days, or in the refrigerator for up to a week. They also freeze beautifully for up to 3 months.
Should you need more inspiration for gluten-free cooking, these other recipes might be just what you’re looking for: Gluten-Free Corn Muffins, Gluten Free Pumpkin Muffins, Gluten Free Chocolate Chip Muffins.

Your Burning Questions Answered!
What makes zucchini muffins moist?
The zucchini itself is the secret! Even after squeezing, it releases a lot of moisture as it bakes. This is what makes these Gluten Free Chocolate Zucchini Muffins so incredibly moist and gives them their signature fudgy texture, all without adding any vegetable taste.
Can I make these muffins with a different flour?
This specific Gluten Free Chocolate Zucchini Muffins recipe was developed to work with the unique properties of almond flour, which provides moisture, structure, and a tender crumb. Using a different flour like oat flour or a gluten-free all-purpose blend would likely require significant adjustments to the liquid ingredients to achieve a similar result.
How do you shred zucchini for muffins?
The easiest method is to use the small-holed side of a standard box grater. This creates fine shreds that melt seamlessly into the batter. There’s no need to peel the zucchini first, as the skin is tender and contains extra nutrients. Just be sure to trim off the ends before grating.
Dig In & Enjoy!
You now have the perfect recipe for rich, chocolatey, and secretly healthy treats. These Gluten Free Chocolate Zucchini Muffins are a fantastic way to sneak in some extra veggies and satisfy your sweet tooth at the same time. Enjoy!
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The Best Gluten Free Chocolate Zucchini Muffins (So Fudgy!)
- Total Time: 31
- Yield: 12 1x
Description
These Gluten Free Chocolate Zucchini Muffins are unbelievably moist, rich, and fudgy. Made with almond flour and packed with chocolate, they’re a secretly healthy treat that tastes like a decadent brownie.
Ingredients
2 cups almond flour
1/3 cup cocoa powder
1/2 tsp baking soda
1/4 tsp salt
3 eggs
1/4 cup coconut oil, melted
1/3 cup maple syrup
1 tsp vanilla
1 cup finely shredded zucchini, squeezed in a paper towel to release extra moisture
1 cup chocolate chips, divided
Instructions
1. Preheat oven to 350F and line a 12-cup muffin tin with cupcake liners or non-stick spray.
2. In a small bowl, whisk together almond flour, cocoa powder, baking soda, and salt. Set aside.
3. In a large bowl, whisk eggs. Add in coconut oil, maple syrup, and vanilla, and stir until well combined.
4. Add the dry ingredients to the wet ingredients and stir until just combined.
5. Fold in the squeezed zucchini, and then half of the chocolate chips.
6. Scoop batter into the muffin tin until each cup is 3/4 full. Top the muffins with the remaining half of the chocolate chips.
7. Bake for 19-21 minutes or until a toothpick inserted in the middle comes out clean. Let cool in the pan for a few minutes before transferring to a wire rack.
Notes
Squeeze the Zucchini: This is the most important step! Removing excess moisture from the shredded zucchini prevents the muffins from being too dense or wet.
Storage: Store completely cooled muffins in an airtight container at room temperature for up to 3 days or in the refrigerator for up to a week. They freeze beautifully for up to 3 months.
- Prep Time: 10
- Cook Time: 21
- Category: Snack
- Method: Baking
- Cuisine: American
Nutrition
- Serving Size: 1 muffin
- Calories: 288
- Sugar: 16.8 g
- Sodium: 120.2 mg
- Fat: 14.7 g
- Carbohydrates: 22.7 g
- Protein: 6 g
- Cholesterol: 46.5 mg