Gluten Free Chocolate Zucchini Muffins (Small Batch Recipe)

These Gluten Free Chocolate Zucchini Muffins are rich, moist, and of course, chocolatey - one of the tastiest ways to use up extra zucchini. The shredded zucchini melts right into the batter, keeping the muffins soft and tender without making them taste like “health food.” They’re perfect for a quick and easy breakfast, or just a little something sweet during the day.

Recipe Ingredient Notes

Gluten Free Flour: I have tested this recipe for gluten free chocolate zucchini muffins with my own gluten-free flour blend and Bob’s Red Mill 1-to-1. Both flour blends produced a tender, moist crumb, and exceptional flavor. I am not saying other brands will not work in this recipe. I just have not tested them in this application. 

Dutch Processed Cocoa Powder: Be sure to use dutch processed cocoa powder, which gives the muffins a richer, fudgier flavor.

Zucchini: When it comes to choosing the zucchini for gluten free chocolate zucchini muffins, using smaller zucchinis is better. Smaller zucchinis have more moisture and sweetness, while supersized zucchinis can be dry and bitter. Plus large zucchini can have seeds, which is not something you want in your muffin batter.

Greek Yogurt or Sour Cream: Greek Yogurt or Sour Cream not only provides flavor but also fat. I have tested this recipe with greek yogurt and sour cream and both products work interchangeably.

Oil: I use grapeseed oil here, but a neutral oil such as vegetable oil or even a mild olive oil will work just fine.

Chocolate: I like using a chopped dark chocolate bar here instead of chips - it melts into the muffin batter and gives you those perfect, gooey pockets of chocolate in every bite.

Make Muffin Liners with Parchment Paper

I have to admit, even though I bake almost daily, I don't always have muffin liners on hand. This is why I love making them with just a sheet of parchment paper at home. You will also need a ruler, a small glass, jar, or measuring cup (with a base that fits into the muffin cups), and a pair of scissors or sharp knife.

1. Cut the parchment paper into 4 x 4 to 4.5 x 4.5 squares. I like doing this by folding the parchment paper so you have a strip of paper that is about 4-4.5" inches wide and 16 inches long. I then fold the parchment strip 3 tips creating the squares. There will be extra parchment paper you can discard. But this is a lot easier than measuring out every piece of paper.
2. Place a parchment square over one muffin cup in the tin. Ensure that it's centered.
3. Take the small glass or object and place it in the middle of the parchment paper square inside the muffin cup. Gently press down to shape the paper around the sides of the cup. I like to wiggle the glass a bit to ensure the muffin liner stays in the muffin tin.
4. Repeat the process for each muffin cup, using a new parchment paper square for each one.
5. After these steps, your homemade paper liners will be ready to use!

Gluten Free Chocolate Zucchini Muffins

These Gluten Free Chocolate Zucchini Muffins come together quickly in just one bowl - and you can mix the batter by hand. No stand mixer (or even a hand mixer) required. Just be sure to use a fine grater for the zucchini.

1. Step 1: In a small bowl, whisk or sift together the gluten free flour, cocoa powder, baking soda and kosher salt. Set aside.

2. Step 2: Finely grate the zucchini using the smallest setting on a box grater, set aside. There is no need to squeeze out the moisture or pat it dry.

3. Step 3: In a separate mixing bowl combine the brown sugar, sour cream, oil, vanilla extract and room temperature large egg. With a whisk combine the ingredients until smooth.

4. Step 4: Add the dry ingredients to the wet ingredients and whisk together. You may need to switch to a flexible spatula if the batter for chocolate zucchini muffins becomes too thick to whisk.

5. Step 5: With a flexible spatula, fold the shredded zucchini into the cake batter. Make sure they are evenly distributed.

6. Step 6: Lastly, fold about 50 grams of chopped dark chocolate or chocolate chips into the gluten free chocolate zucchini muffin batter. Reserve some for sprinkling the muffins before baking.

7. Step 7: Divide the chocolate zucchini muffin batter between the papers with the large cookie scoop. I fill mine almost to the rim. This way, they will have a beautiful bakery-style dome. Top them with some additional chocolate if you like.

8. Step 8: Bake the Gluten Free Chocolate Zucchini Muffins for 8 minutes at 425°F. Then reduce the oven temperature without opening the oven door to 350°F and bake for an additional 12-13 minutes or until a toothpick comes out clean. Allow the muffins to cool in the muffin tin for 5-10 minutes before transferring them to a cooling rack.

Storage & Freezing

Store the gluten free chocolate zucchini muffins in an airtight container at room temperature for up to 3 - 4 days. While most muffins are best the day they are baked, these were delicious the day after.

To freeze the gluten free zucchini muffins, place them on a sheet tray and pop them in the freezer for 30-45 minutes or until they are solid. Once frozen, transfer them to an airtight container or freezer bag and freeze for up to 3 months. When ready to eat, allow them to thaw at room temperature or nuke in the microwave for 15-30 seconds.

Note about Salt in my Recipes

I use Diamond Kosher Crystal Salt in all of my recipes unless otherwise stated. If use use a different brand or kind of salt in your kitchen please adjust accordingly since some salts can be saltier. If you use Morton’s Kosher Salt please be aware that their salt granules are smaller in size, denser, and crunchier and twice as salty.

Baking in grams

I share my recipes in grams and by weight since baking by weight is the most accurate way to bake. Digital Scales are very affordable and easy to use. You can purchase them on Amazon for less than a set of measuring cups. For small amounts under 10 grams, I like to use this Precision Pocket Scale. Measuring cups are very inaccurate which can cause significant errors when it comes to gluten-free baking or baking in general. Especially since I bake with gluten-free flours which weigh differently than “regular” flours. I do provide some ingredients like spices and leavening agents in measuring spoons. To learn more about Baking with a digital scale, make sure to check out my post about Baking by weight.

Note about Ovens and Oven Temperatures

All my recipes are tested and developed with a conventional oven. I always bake my baked goods on the rack placed in the MIDDLE of my oven. This way the heat coming from the bottom will not burn my baked goods.

If you are baking with convection (fan-forced), please adjust the recipes accordingly. Convection oven can cause baked goods to dry out quickly and still be raw inside. Since takes at least 15-20 minutes for a standard American Oven to be fully preheated. I highly recommend investing in an Oven Thermometer.

Substitutions and Modifications

Any dietary or ingredient modifications/substitutions to this recipe may alter the end result in appearance and taste. I test my recipes several times as published in this post and The Gluten Free Austrian Blog is not responsible for the outcome of any recipe you find on our website.