Zucchini Carrot Gluten Free Mini Muffins

5 from 7 votes
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Gluten Free Carrot Zucchini Muffins are a tasty and surefire way to get the kids devouring their veggies. Sweetened only with a bit of maple syrup, loaded with vegetables, and made with a simple blend of gluten free flours, these mini muffins are a bite-sized breakfast or snack you can feel good about feeding the kiddos.

Gluten Free Carrot Zucchini Muffins

[adthrive-in-post-video-player video-id="uM9SH5PJ" upload-date="Mon Jun 18 2018 00:00:00 GMT+0000 (Coordinated Universal Time)" name="Carrot Zucchini Mini Muffins" description="With whole wheat and gluten free versions, these Carrot Zucchini Mini Muffins are a healthy breakfast or snack that are a kid-favorite and mom-approved."]

So many people have left comments about my whole wheat Healthy Carrot Zucchini Mini Muffins being the only way they get their picky kids to eat vegetables. So I figured it was time to make a gluten-free version.

I’ve been making the whole wheat version for years. And if you check out that post, you can see all the comments from people who have made them and gotten kids who wouldn’t touch a green vegetable to devour them. It’s no wonder they have been one of my most popular recipes of all time.

It was only these muffins, Air Fryer Gluten Free Zucchini Fritters, and Zucchini Tater Tots that got my kids to eat zucchini when they were little. Now they love the gluten free muffins as much as the original ones, and two batches disappeared in no time.

three gluten free carrot zucchini muffins on a platter with one leaning against the others

Why Do We Love these Gluten Free Mini Muffins?

This healthy muffin recipe makes a bite-sized snack perfect for little fingers, but people of all ages still love them. With plenty of shredded carrots and zucchini, it’s a sneaky way to get the kids to eat their vegetables. Since they are also nut-free, they are perfect to pack in a lunchbox and send to school or camp as an easy kids lunch idea when everyone is tired of sandwiches. Or grab them as a quick breakfast on a busy morning.

While you are likely to devour them right away, these gluten free mini vegetable muffins freeze well. So you can make a bunch when you have an overabundance of zucchini in the summer to have on hand for snacks all year round.

They are super quick and easy to make, too. Even in the middle of refereeing kiddo chaos, I can make a batch.

Just as in the original recipe, all you do is sift together the dry ingredients, which in this case includes a mixture of brown rice flour, tapioca starch, and potato starch instead of white whole wheat flour. Then mix the wet ingredients together, and fold in the dry ingredients. Stir in a heap of shredded zucchini and carrots (no, you don’t even have to squeeze out the excess moisture), plus some raisins, and bake.

You might think it’s an awful lot of carrots and zucchini being held together by just a little batter but just fill a 24-cup mini muffin tin and they will bake up perfectly. These mini muffins will be fully loaded with veggie goodness, but you don’t have to tell the kiddos. Yes, they are actually picky kid-approved!

gluten free zucchini carrot muffins in a mini muffin tin


  • Gluten free flour – the gluten free flour mixture is a simple blend of brown rice flour, tapioca starch, and potato starch
  • Cinnamon
  • Salt
  • Baking soda
  • Butter – melted and cooled
  • Maple syrup – you can also use honey to sweeten these mini muffins, but I prefer maple syrup, and I only use maple syrup from Vermont
  • Egg
  • Vanilla extract
  • Zucchini – finely grated, but you fo NOT need to squeeze out the excess moisture
  • Carrots – finely grated, but you fo NOT need to squeeze out the excess moisture
  • Raisins
bowls of gluten free flours, shredded carrots and zucchini, vanilla extract, raisins, and melter butter, a pitcher of maple syrup, and egg, and measuring spoons of cinnamon, salt, and baking soda on a marble tabletop

How to make them

  1. Preheat your oven to 350°F and coat a mini muffin pan with nonstick cooking spray.
  2. Sift or whisk the dry ingredients together in a bowl and set aside.
  3. In a large bowl, whisk together the butter, maple syrup, egg, and vanilla extract.
  4. Gently stir the dry ingredients into the wet ingredients until just barely combined.
  5. Fold in the zucchini, carrots, and raisins.
  6. Scoop into the prepared pan and bake for 15-20 minutes or a toothpick comes out clean.
  7. Cool for a few minutes and remove from the pan.

Tips for Success

  • I simply coat my muffin pan with nonstick spray. I’ve never use cupcake liners and I’ve never had a problem with sticking.
  • As with all gluten free baking recipes, be sure to lightly spoon the flours and starches into the measure cups and level off with a knife. Then you can either sift or whisk all the dry ingredients together.
  • I like maple syrup, but you can also use honey in this recipe.
  • The carrots and zucchini should be finely shredded, but there is no need to squeeze out the excess moisture.
  • It might seem like a lot of veggies with just a little batter, but trust me. Divide it evenly between a 24-cup mini muffin tin and you’ll be just fine.
three gluten free mini muffins on a platter in front of a pan of more carrot zucchini muffins

Freezing mini muffins

These vegetable muffins freeze well. That makes them a perfect way to use up all the summertime bumper crops of zucchini when everyone is looking for more zucchini recipes. In an airtight container, they will last up to 2 to 3 months. In fact, they are safe to eat for much longer, but after time they can start to get dry or have their flavor impacted. 

That being said, if you are only going to take out a couple at a time, I do recommend wrapping them individually or several together. Then place them in a zip-top plastic freezer storage bag or another airtight container. You can toss them all in one bag or container, but each time you open it, you’ll introduce moisture, which could lead to moisture condensing and freezing in the bag, or freezer burn.

I usually place four to six muffins in a plastic sandwich bag, then put all of the sandwich bags in one big freezer storage bag. Then I can pull out one small bag at a time without affecting the rest of the muffins. 

one gluten free mini muffin broken in half on a slate platter

Things You’ll Need

Brianne Recommends
  • Start with the basics, including two bowls, a spatula, and measuring cups and spoons.
  • I like to use a small scoop to fill the mini muffin tin.
  • A box grater with a side for finely shredding is perfect for finely grating the carrots and zucchini.
three gluten free mini vegetable muffins on a tray with a carrot and zucchini nearby
5 from 7 votes

Healthy Carrot Zucchini Mini Muffins

Kid-favorite and mom-approved gluten free mini muffins are sweet, moist, and packed with veggies, naturally sweetened with only a bit of maple syrup or honey. These freezer-friendly muffins make a yummy and healthy breakfast or snack.
Prep: 15 minutes
Cook: 20 minutes
Total: 35 minutes



  • Preheat oven to 350°F and place rack in the center of the oven, and coat a mini muffin pan with nonstick cooking spray.
  • Sift or whisk together the brown rice flour, tapioca starch, potato starch, cinnamon, salt, and baking soda in a mixing bowl and whisk until thoroughly combined. Set aside.
  • In a large mixing bowl, stir together the butter, maple syrup (or honey), egg, and vanilla extract.
  • Add the flour mixture to the wet ingredients and stir together until just barely combined.
  • Add the zucchini, carrot and raisins and stir gently until just distributed.
  • Fill each cup in the mini muffin pan approximately ¾ full (I use a small cookie scoop slightly overfilled).
  • Bake for 15-20 minutes or until a toothpick inserted in the center of a muffin comes out clean.
  • Let cool slightly before running a butter knife around the edge and removing the muffins from the pan.
Nutrition Facts
Healthy Carrot Zucchini Mini Muffins
Amount Per Serving (1 muffin)
Calories 70 Calories from Fat 9
% Daily Value*
Fat 1g2%
Cholesterol 10mg3%
Sodium 89mg4%
Potassium 97mg3%
Carbohydrates 12g4%
Sugar 4g4%
Vitamin A 520IU10%
Vitamin C 2.1mg3%
Calcium 13mg1%
Iron 0.3mg2%
* Percent Daily Values are based on a 2000 calorie diet.


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  1. Michele

    I really like this recipe and have a question for the next time i make them – I couldn’t find tapioca starch so I used tapioca flour. Are these interchangeable? There was something that tasted a little bit bitter in these muffins and I cannot quite figure out where that comes from. I bought brown rice flour, tapioca flour and potato starch specifically for this recipe, so i know they are not out of date. Thanks for any information you can provide!

    1. Brianne Cupcakes & Kale Chips

      Thank you so much for letting me know this, Tayy. I’m happy that you were able to make it egg-free!

    1. Brianne Cupcakes & Kale Chips

      Thank you, Shelli! I’m so glad to hear that you and your sons enjoyed the muffins. Thank you for rating the recipe, too!

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