Making the best gluten-free zucchini muffins has never been easier or flawless using these easy baking tips! Learn how to make zucchini muffins with gluten-free flour with perfect moist, light, and fluffy results. Follow three simple steps – blotting zucchini, letting the batter rest, and baking at a lower temperature – to become an effortless gluten-free muffin expert!

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Perfectly Moist & Fluffy Gluten-Free Zucchini Muffins
Even with tons of gluten-free muffin recipes, it’s hard not to come back to these fluffy, moist gluten-free zucchini muffins time and again.
What makes this recipe stand out above all others? While most zucchini muffin recipes are quick and simple, many don’t account for the extra moisture zucchini adds, particularly throwing off the balance when making zucchini muffins with gluten free flour.
To counteract this, I turned to some of my favorite techniques for gluten-free baking. To make a light, fluffy zucchini muffins gluten free, simple tricks, like letting the batter rest, baking at a lower temp, and squeezing the zucchini slightly dry (easy trick for my favorite almond flour zucchini bread recipe as well), give a taste and texture identical to traditional ones.
Below I share more on why this method works, as well as many more baking, storing, and freezing tips. Also, be sure to check out the included modifications, turning these GF zucchini muffins into many more creative versions. It’s all here!
These are absolutely wonderful! I have to be gluten free due to celiac so these were a healthy dream come true! I used some frozen blueberries and pecans. The blueberries stayed nice and juicy. I am making them again and it has only been a week.
—Elizabeth
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Ingredient Tid Bits
While the ingredients are simple, the magic happens in the technique. Below I share any workable substitutions and how the ingredients contribute to the recipe’s success.
- Zucchini – Grate with box grater or a grater disc on a food processor with the skin on. Soak up extra moisture by blotting grated zucchini dry with paper towels or a dish towel before adding to batter. This also works really well when making chewy, homemade gluten-free zucchini cookies as well.
- Egg – For a vegan version, use an egg replacer, such as flax egg.
- Brown sugar – Adds a caramel flavor and slight chewiness. You may reduce slightly for less sugar or replace with coconut sugar.
- Oil – Use any oil that floats your boat – vegetable, melted coconut, canola, avocado. Because no butter is used, these muffins are dairy-free as well.
- Gluten-free all purpose flour – I highly recommend Cup4Cup gluten-free flour for best results, but you can also take a peek at the readers’ comments below for other workable flour blends.
- Mini chocolate chips – If you would like to make chocolate chip zucchini muffins, I highly recommend using mini chocolate chips so the chocolate disperses evenly. Regular baking chips have a tendency to sink to the bottoms of the muffins.
Tip #1 – Blot Zucchini
Rather than grating the zucchini and immediately adding it to the batter, first gently blot, squeezing in paper towels or a clean, lint free dish towel. Why is this step crucial when making GF muffins?
GF flour starches already struggle with absorbing moisture and zucchini is made primarily of water. Removing some of zucchini’s excess moisture means a light, moist crumb, but without being overly dense and heavy. Plus no more sunken middles!

Tip #2 – Let Muffins Rest Before Baking
When I began experimenting turning this homemade gluten-free zucchini bread into muffins, I prepared the batter identically and distributed it a muffin tin. After they were pulled from the oven, the muffin tops shriveled and looked overly wet.
Why did this happen with the muffins but not the bread? Zucchini bread has a much longer cook time than muffins, giving time for the starches to fully hydrate and soak up the liquids. Therefore, letting the batter sit before baking gave the extra time needed for them to bake up round and fluffy.
Therefore, prepare the batter and pour it in the muffin pan. While the oven preheats let them sit for 15-20 minutes, which gives a head start on absorbing the liquids. Do not let them sit much longer than that or they will become too dry or may not rise. This easy trick worked wonders on my bakery-style gluten free yellow layer cake as well!

Tip #3 – Bake At A Lower Oven Temperature
Typically muffin recipes use a higher oven temp between 375ºF-400ºF. This helps them rise quickly and set the upper crust. When trying this with gluten-free muffins, they looked beautiful in the oven, but then quickly deflated.
While a lower oven will not give quite as dramatic of domed top, a longer, gentler bake time solidifies the muffins shape so they do not shrink once you pull them from the oven. It also adds additional cook time, which helps the GF flour fully emulsify with the liquids, yielding a soft, fluffy crumb.
So. Many. Add-In ideas
If you would like something besides chocolate chip zucchini muffins, try one of the suggestions below. Stir these in after the dry ingredients have been added. Drop me a line in the comments below if you have any additional ideas!
- 1/2 cup chopped pecans or nuts
- 2 teaspoons lemon or orange zest
- 1 cup fresh or frozen blueberries
- 1/2 cup chopped walnuts
- 1/2 cup chopped raisins
- 2/3 cup sweetened shredded coconut

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Did you make this recipe? I love hearing from you! Leave a star rating and comment below the recipe card. It helps others when searching for recipes and I appreciate feedback from our community. You will always hear back from me! -Melissa

Moist Gluten-Free Zucchini Muffins with Oil
Ingredients
- 2 cups (340 g) grated zucchini , about 1 medium
- 1 large egg
- ½ cup (100 g) granulated sugar
- ½ cup (117 g) packed brown sugar
- ¼ cup (55 g) oil, any preferred
- 2 teaspoons vanilla extract
- 1 ½ cup (214 g) all purpose gluten free flour, Cup4Cup brand is recommended
- 1 teaspoon baking powder
- ½ teaspoon baking soda
- 1 ½ teaspoon ground cinnamon
- ½ cup (optional) miniature semi-sweet chocolate chips
Equipment
Instructions
- Line standard-size muffin cups with paper liners or grease with nonstick cooking spray. The oven preheats later while the muffin batter rests. (This allows time for the gluten-free starches to soften and hydrate with the liquids.)
- Grate zucchini and lay in a double layer paper towel or dish towel. Squeeze gently to soak up excess water and set aside.2 cups grated zucchini
- In a large bowl whisk together egg, sugar, packed brown sugar, vegetable oil, and vanilla extracts. Stir in slightly dried zucchini.1 large egg, ½ cup granulated sugar, ½ cup packed brown sugar, ¼ cup oil, 2 teaspoons vanilla extract
- Add flour, baking powder, baking soda, and cinnamon. Stir until very well combined, and no flour pockets remain. If using chocolate chips, stir in.1 ½ cup all purpose gluten free flour, 1 teaspoon baking powder, ½ teaspoon baking soda, 1 ½ teaspoon ground cinnamon, ½ cup (optional) miniature semi-sweet chocolate chips
- Preheat the oven to 350°F. While the oven is preheating, use a large trigger scoopto distribute the batter between the muffin cups or fill each cup about ⅔ full. The muffins should sit 15-20 minutes before baking.
- Bake for 23-25 minutes, our until the tops are set and lightly spring back when touched. Cool in pan for 5 minutes before turning onto a wire rack.
Notes
Dairy-Free Note
If you are making gluten-free zucchini chocolate chip muffins, be sure to use dairy-free chocolate chips, such as Enjoy Life mini chocolate chips. Also, be sure to read the ingredient label on the GF flour because some blends do contain milk powder.Storing and Freezing
Once they have completely cooled store in an airtight container up to 2 days at room temperature. Do not store in the fridge, or they will dry out. For optimal freshness, I freeze gluten-free muffin leftovers right away since they don’t stay fresh as long. Wrap the muffins in plastic wrap and place in a freezer-safe container or freezer bag up to 3 months.This post contains affiliate links. My opinions are always my own. If you purchase a product through an affiliate link, I make a small commission – at no cost to you. Read full disclosure policy here.



🇨🇦I made these and despite having an oven issue which meant they stood in the muffin tin for over an hour, they were perfect.
For those in Canada I used Robin Hood gluten free flour and other than using almond extract instead of vanilla I followed the recipe as written.
Thank you for sharing this, Donna! I will make a note myself for Canadian community members who want to know which flour blend they can use.
Best,
Melissa
I’m hosting and two friends have gluten allergies. One is allergic to eggs and another to milk so this recipe is perfect. I used a chia egg and I couldn’t find chocolate chips without traces of milk so I used raisins instead. The raisins turned out to be a great substitute. I think I would use less sugar next time but that’s a personal preference. My kid is also gluten intolerant so I’ll freeze the leftovers for our household.
These came out so good! I’m hosting and two friends have gluten allergies, one is allergic to eggs, and another to milk so this recipe was perfect. I used a chia egg and I couldn’t find chocolate chips without traces of milk so I went with raisins instead. The raisins worked well. My kid is also gluten intolerant so I’ll freeze the leftovers for our household.
So lovely to hear, Leeanne! What a good friend you are to make adaptations for them. I know from my own experience with allergies that is always appreciated immensely!
Best,
Melissa
These were delicious and we will make them again. We ended up only having 1/2 c. of GF all purpose flour so supplemented with 1/2 c. each of oat and almond flour. We used coconut for the oil.
Hi Anne & Eloise,
I love that you were able to substitute with the additional flour types to make them work with what you have on hand! Thanks for sharing!
Best,
Melissa
These muffins are delicious! ❤️
Thank you, Kelly! I appreciate it!
Best,
Melissa
Great recipe. They are moist and have a good texture. I added only half the amount of cinnamon so I could add 1/4t each cardamom & allspice. The spice combo is delicious. Took another rater’s suggestion to add blueberries—good call. Poked 4 blueberries (along with a bit of chopped walnuts) into each filled muffin cup. I like to add them after the batter is placed in the cup so that each muffin will be the same. Thanks for the recipe.
Sounds like all great additions! Thank you so much for taking the time to share!
Best,
Melissa
These are absolutely wonderful! I have to be gluten free due to celiac so these were a healthy dream come true! I used some frozen blueberries and pecans. The blueberries stayed nice and juicy. I am making them again and it has only been a week. I plan to try adding some flax seed (ground) for extra nutrients.
Love hearing this, Elizabeth! Thanks so much for sharing!
Best,
Melissa
Hi Melissa – I am enjoying your posts and trying your recipes! (You have made me laugh out loud with your podcasts, so thank you). I recently tried this zucchini muffin recipe and have some questions: I didn’t see any salt called for, so I added 1/2 tsp. Also, I used King Arthur’s 1-to-1 gf flour – I avoid dairy- and the amount specified for Cup4Cup was too much; I think next time, I would start with 1 cup and progress with adding a little more, if needed. Would you consider listing the amount of flour in grams? I bought a digital, kitchen scale when I switched to gf and it has really helped me. Thanks!
Hi Martha!
I’m so glad you wrote! This is a great question. Although it is more accurate to bake from weight, the reason I don’t do it is because gluten-free flours weigh differently since they are all made up of different compositions. For instance, I use Cup4Cup pretty much exclusively in my recipes, which weighs 140g per cup. King Arthur Measure for Measure weighs 120g per cup. Since people use the flours that work best for them, it’s hard to land on a universal weight. Unfortunately this is also why some people get different consistencies of batter (and the recipe gets blamed 🙁 )
As for the salt, I adapted the recipe from the bread, which also doesn’t have any, but it doesn’t hurt to add some! I’m so glad you are enjoying the podcasts. It means a lot!
Best,
Melissa