Gluten Free Carrot Zucchini Muffins

5 from 7 votes
(Click the stars to vote)
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Picky kids and adults love these Gluten Free Carrot Zucchini Muffins! They may be mini muffins, but they are packed with veggies! It’s a bite-sized breakfast or snack you can feel good about feeding the kiddos since they have lots of vegetables, but are sweetened with only a bit of maple syrup.

three gluten free carrot zucchini muffins on a slate platter with one split in half

Why You’ll Love These Gluten Free Mini Muffins

  • Cuisine Inspiration: American
  • Primary Cooking Method: Oven
  • Dietary Info: Gluten-free, Dairy-free option
  • Skill Level: Easy

So many people love my original Carrot Zucchini Muffins made with whole wheat flour that I had to make them into gluten free mini muffins. Those muffins have gotten so many picky kids to eat vegetables that the GF kids and moms needed an easy snack solution too. Here’s why these are sure to be a hit in your house…

  • So many veggies. It seems like a lot of carrots and zucchini being held together by just a little batter, but if you fill a 24-cup mini muffin tin, they will bake up perfectly and fully loaded with veggie goodness.
  • Kid-approved. They may only have a little maple syrup, but they have just enough sweetness to entice the kiddos despite those sneaky vegetables.
  • Freeze well. They are a perfect way to use up all the summertime bumper crops of zucchini when everyone is looking for more zucchini recipes.
  • Lunchbox-friendly. The small size makes them a great packable snack or easy kids lunch idea. But the other advantage is that they have no nuts, making them perfect for a nut-free school environment. They are also adaptable to other allergies since they are gluten free and can easily be made with substitutes for the butter and eggs.

Loved this recipe! So easy and very delicious. My sons loved these muffins as well! -Shelli

Easy, delicious and a great snacking muffin when on the go. Thank you! -Liana

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

Gluten Free Carrot Zucchini Muffin Ingredients

A couple of veggies and basic pantry ingredients are all you need to whip up a batch of these gluten free mini muffins. Here’s a quick overview of what you’ll need. The full quantities are listed in the recipe card at the bottom of the post.

  • Gluten free flour – the gluten free flour mixture is a simple blend of brown rice flour, tapioca starch, and potato starch. You can also replace these flours and starches with 1:1 GF baking flour.
  • Cinnamon
  • Salt
  • Baking soda
  • Unsalted butter – melted and cooled. You can substitute vegan butter for a dairy-free option.
  • 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 – lightly beaten.
  • Vanilla extract
  • Zucchini – finely grated, but you do NOT need to squeeze out the excess moisture.
  • Carrots – finely grated, but again, it is NOT necessary 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 Gluten Free Mini Muffins

These muffins are so easy to make. Preheat your oven and grease your mini muffin pan. Then I’ll give you a brief rundown, but be sure to follow the detailed instructions at the bottom of the post.

  • Make wet and dry mixtures. Sift or whisk the dry ingredients together in a bowl and set aside. Then in a large bowl, whisk the melted butter, maple syrup, egg, and vanilla extract.
  • Mix the muffin batter. Gently stir the dry ingredients into the wet ingredients until just barely combined. Fold in the zucchini, carrots, and raisins.
  • Fill the pan. Scoop into the prepared pan, dividing the batter evenly between the 24 wells.
  • Bake and cool. Bake the muffins in the 350°F oven for 15-20 minutes or a toothpick comes out clean. Cool for a few minutes and remove the carrot zucchini muffins from the pan.
gluten free zucchini carrot muffins in a mini muffin tin

Tips for the Best GF Muffins

Here are a few things to keep in mind when you make carrot zucchini muffins:

  • Don’t get stuck. I’ve never use cupcake liners and I’ve never had a problem with sticking. I simply coat my muffin pan with nonstick spray.
  • Measure carefully. 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.
  • Meet your needs. You can use the individual flours and starches or a 1:1 four. Vegan butter will work fiune, Honey can be swapped for the maple syrup. And while I haven’t tested it, I suspect different egg substitutes for baking will work well.
  • Shred, don’t squeeze. The carrots and zucchini should be finely shredded. A box grater with a side for finely shredding is perfect. There is no need to squeeze out the excess moisture. It actually helps keep the muffins moist.
  • Don’t panic. 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 (I like to used a small scoop) and you’ll be just fine.

three gluten free mini muffins on a platter in front of a pan of more carrot zucchini muffins

Storing Gluten Free Mini Muffins

Countertop. In an airtight container, you can store the muffins at room temperature for a couple of days. I wouldn’t leave them out much longer because all of the moisture from the veggies can cause them to get moldy very quick.

Refrigerator. You can refrigerate the gluten free carrot zucchini muffins for up to 4 or 5 days, and possibly even a week if they are sealed properly.

Freezer. You can also freeze them for up to 2 to 3 months wrapped tightly in plastic wrap, plastic freezer storage bags, or an airtight container. 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. This allows you to pull out just a few at a time without affecting the rest of the batch.

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

More Gluten Free Muffin Recipes

a pan of gluten free mini carrot zucchini muffins with three on a slate tray in front of it
5 from 7 votes

Gluten Free Carrot Zucchini Muffins

Picky kids and adults love these Gluten Free Carrot Zucchini Muffins! They may be mini muffins, but they are packed with veggies! It's a bite-sized breakfast or snack you can feel good about feeding the kiddos since they have lots of vegetables, but are sweetened with only a bit of maple syrup.
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.


You can also replace the brown rice flour, tapioca starch, and potato starch with 1 cup plus 2 Tablespoons Gluten Free 1:1 Baking Flour.
Nutrition Facts
Gluten Free Carrot Zucchini 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.
Disclaimers: Please discuss your individual dietary needs (i.e. gluten free) with a physician. Even when not specified, be sure to verify all ingredients are gluten free, if needed, by reading labels on all packaging and/or confirming with the manufacturer this varies by brand and can change at any time. Nutrition information shown is an estimate and not guaranteed to be accurate.


  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!

5 from 7 votes (3 ratings without comment)

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