Gluten Free Zucchini Muffins

5 from 1 vote
A red circle with the letters GF

This post may contain affiliate links. Read my disclosure policy.

Moist and tender Gluten Free Zucchini Muffins are studded with chocolate chips and crunchy walnuts, with just the right amount of maple syrup for a hint of natural sweetness. Celebrate summer squash season with these cozy zucchini gluten free muffins that come together fast.

A big bowl of zucchini muffins with chocolate chips.

Why You’ll Love These Gluten Free Zucchini Muffins

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

I carefully developed these gluten free zucchini muffins to achieve a gorgeous domed top and a moist, fluffy interior, and you’ll love the results! The right blend of applesauce and oil adds natural sweetness and fat so that the muffins never dry out. Then you’ll stir in maple syrup, cinnamon, and nutmeg for a gorgeous depth of flavor. I also threw in a few toasted walnuts and chocolate chips for crunch and, well, chocolate! Here’s why you’ll love these zucchini muffins gluten free:

  • So tender. There’s nothing worse than a dry muffin! Because of the applesauce, maple syrup, and oil, these zucchini muffins remain soft and moist, even though they are gluten free.
  • They’re easy to make. Browse the ingredients list below and you’ll quickly see that you don’t need anything fussy to put the batter together. And, you can easily use a whisk to mix the batter if you don’t feel like taking out the mixer.
  • Great use of zucchini. I love adding vegetables to sweet (or lightly sweet) bakes, and this recipe makes the best of the zucchini season. But, you use just enough squash for a slight hint of flavor without it being an overly squash-flavored muffin. In other words: muffin perfection.
A perfectly domed gluten free zucchini muffin on a plate.

Recipe Ingredients

I’ve included some notes below along with the ingredients to help you make these gluten free zucchini muffins. Be sure to check the recipe card at the end of this post for the full ingredient amounts.

  • Gluten Free Flour: Use a 1:1 gluten free flour for these muffins. I recommend Bob’s Red Mill 1-to-1 Gluten Free Baking Flour.
  • Ground Spices: A cozy duo of cinnamon and nutmeg adds warmth to these zucchini gluten free muffins.
  • Leavening: A combination of baking powder and baking soda creates muffins with a perfect domed top.
  • Salt
  • Maple Syrup: If needed, you can substitute an equal amount of light or dark brown sugar.
  • Oil: I use avocado oil in this recipe, or you can use vegetable oil.
  • Applesauce: Unsweetened applesauce is preferable so that it doesn’t overly sweeten the muffins.
  • Granulated sugar
  • Eggs: I always use large eggs in my baking recipes, and you’ll use large eggs to make these muffins. If needed, you can try one of these egg substitutes for baking.
  • Vanilla Extract
  • Zucchini: For these muffins, you won’t need to deal with squeezing out any excess water from the zucchini, which streamlines the process.
  • Chocolate Chips: Use your choice of chocolate chips – I like semisweet chocolate chips – dairy-free if needed to make this recipe completely without dairy.
  • Walnuts: Toasted walnuts add texture. You can substitute another toasted nut of your choice. Omit them or try pumpkin seeds if you have a nut allergy.
  • Sanding Sugar: This can be used as an optional topping.  
Ingredients for gluten free zucchini muffins are shown portioned out and labelled: zucchini, sugar, eggs, nutmeg, salt, baking powder, gluten free flour, maple syrup, chocolate chips, walnuts, vanilla.

How To Make Gluten Free Zucchini Muffins With Chocolate Chips

These easy muffins come together in a snap and are super uncomplicated. I’ve outlined how to make them in the photos below. Find the detailed instructions in the recipe card lower down.

  • Prepare. Preheat the oven to 425°F and line every other well of two 12-well cupcake pans with cupcake liners.
  • Make the dry mix. Sift together the flour, cinnamon, baking powder, baking soda, salt, and nutmeg into a bowl.
  • Make the wet mix. Beat together the maple syrup, oil, applesauce, granulated sugar, eggs, and vanilla extract.
  • Add the zucchini. On low speed, blend into the zucchini.
  • Combine. Beat in the flour mixture on low.
  • Rest the batter. Allow the batter to sit for 20 minutes to hydrate the flour.
  • Stir in the add-ins. Gently fold in 1⁄2 cup of the chocolate chips and the walnuts.
  • Add to the muffin pan. Place the batter in the prepared pans.
  • Finish with chocolate. Sprinkle the tops of the muffin batter with chocolate chips and sanding sugar if using.
  • Bake. Place the pans in the oven and bake at 425°F for 5 minutes, then reduce the heat to 350°F and bake for 14-17 minutes.
  • Cool. Allow the muffins to cool for 5 minutes in the pan, and then transfer them to a cooling rack.
A gluten free zucchini muffin topped with chocolate in a muffin tin.

Tips & Variations

My friend, Beth, from The First Year Blog, is the Muffin Queen and has mastered the art of the Superdome on her muffins. If there is one thing I know about gluten free muffins, and gluten baked goods in general, is that they do have a tendency to be dense. So as I was working on the perfect balance of ingredients, I consulted her technique to get that lovely domed top, which also means they have achieved a light and tender crumb inside.

Here are her top tips, plus a few of mine:

  • Rest the batter. Beth does this for conventional wheat muffins, but it’s even more important when you bake gluten free muffins because gluten free flour takes longer to absorb moisture. Skipping this step can lead to a grainy texture.
  • Fill every other muffin cup completely. This means you’ll need two pans for a dozen muffins. This gives them space to spread and ensure even heat distribution. You’ll also be filing them nearly to the top. This recipe has the perfect amount of batter for exactly 12 muffins. Don’t panic if they seem too full.
  • Start baking at a high temperature. You’ll begin the baking process at 425°F so that the outside sets quickly, then lower it to 350°F to allow the center to cook through completely as that lovely dome forms.
  • Measure the flour correctly. Be sure to lightly spoon your flour if you are using measuring cups, or even better, use a scale and measure by weight. Don’t use the scoop method!
  • Don’t pack the zucchini tightly. Too much moisture in the batter will lead to dense muffins, so don’t pack the zucchini in too tightly, and measure your applesauce and oil carefully. And, unlike zucchini bread, I prefer to finely grate the zucchini versus doing a coarse shred.
  • Don’t use all applesauce. Don’t be tempted to use all applesauce or all oil. Using an equal blend of applesauce and oil half provides the perfect balance of fat and moisture.

Butter is spread on two halves of a zucchini muffin on a plate.

Proper Storage

You have several options for how to store gluten free zucchini muffins, detailed below:

  • Counter – Place the muffins in an airtight container and keep them on the counter at room temperature for up to 3 days.
  • Fridge – Add the muffins to an airtight container and store it in the fridge for up to 5 days.
  • Freezer – Wrap each muffin in plastic wrap then foil, and place them in a sealable freezer-safe bag. Store the muffins in the freezer for up to 3 months. Make sure to thoroughly thaw the muffins in the fridge before serving.
A bowl of gluten free zucchini muffins topped with chocolate chips.

Make It A Meal

Muffins are a wonderful snack, or you can serve them as breakfast or in addition to other dishes like eggs, bacon, and more. Here are a few serving suggestions for gluten free zucchini muffins:

Gluten free zucchini muffins topped with chocolate chips are shown close up.
5 from 1 vote

Gluten Free Zucchini Muffins

Moist and tender Gluten Free Zucchini Muffins are studded with chocolate chips and crunchy walnuts, plus warming spices, and maple syrup.
Prep: 15 minutes
Cook: 22 minutes
Resting Time 20 minutes
Total: 57 minutes
Servings: 12 muffins


  • 1 ¾ cups 1:1 gluten free flour (260 grams, recommended: Bob’s Red Mill 1-to-1 Gluten Free Baking Flour)
  • 2 teaspoons cinnamon
  • 1 teaspoon baking powder
  • ½ teaspoon baking soda
  • ½ teaspoon salt
  • ¼ teaspoon ground nutmeg
  • ½ cup maple syrup
  • ¼ cup avocado or vegetable oil
  • ¼ cup applesauce
  • ¼ cup granulated sugar
  • 2 large eggs
  • 2 teaspoons vanilla extract
  • 1 cup finely grated zucchini (no need to squeeze out the liquid)
  • ¾ cup chocolate chips , divided (dairy free, if needed)
  • ¼ chopped toasted walnuts
  • Sanding sugar , optional


  • Preheat oven to 425°F and line every other well of two 12-well cupcake pans with cupcake liners.
  • In a medium bowl, sift or whisk together the flour, cinnamon, baking powder, baking soda, salt, and nutmeg. Set aside.
  • In a large mixing bowl, use a hand mixer at medium speed toblend the maple syrup, oil, applesauce, granulated sugar, eggs, and vanilla extract until combined. Reduce the speed to low and blend in the grated zucchini. Turn off the mixer and add the flour mixture to the bowl. Turn on the mixer to low speed and blend until just combined.
  • Cover the mixing bowl with plastic wrap and allow the batter to sit for 20 minutes. This allows the gluten-free flour time to absorb more liquid. Then gently fold in 1⁄2 cup of the chocolate chips and walnuts.
  • Once the batter is ready, fill the lined muffin pans and sprinkle the tops with the remaining chocolate chips and sanding sugar, if desired.
  • Bake at 425°F for 5 minutes. Reduce the oven to 350°F and bake for an additional 14-17 minutes, or until a toothpick inserted comes out clean. Allow the muffins to cool for 5 minutes in the pan, and then transfer them to a cooling rack to cool completely.
Nutrition Facts
Gluten Free Zucchini Muffins
Amount Per Serving
Calories 226 Calories from Fat 81
% Daily Value*
Fat 9g14%
Saturated Fat 3g15%
Trans Fat 0.003g
Polyunsaturated Fat 1g
Monounsaturated Fat 4g
Cholesterol 27mg9%
Sodium 156mg7%
Potassium 164mg5%
Carbohydrates 35g12%
Fiber 2g8%
Sugar 20g22%
Protein 3g6%
Vitamin A 82IU2%
Vitamin C 4mg5%
Calcium 60mg6%
Iron 1mg6%
* 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. Donna

    These look spectacular for a family-pleasing…yet healthy brekkie or brunch…Question….Could I possibly omit the guar gum or use something else to make it “work” as perfectly as you have here?…These look very moist but not dense…Hoping to achieve the same effect. Alas, in France ..special baking “gums” are quite difficult to come by if you live in the boonies….Could ground chia or flax help?…Any enlightenment would be so very appreciated. Thank you for this wonderful share!

Leave a Comment

Recipe Rating

I accept the Privacy Policy