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Meal Type ยป Gluten Free Snacks ยป Gluten Free Chocolate Zucchini Muffins

Gluten Free Chocolate Zucchini Muffins

Claire Cary

By

Claire Cary

5 from 12 votes
February 6, 2021
Jump to Recipe

These gluten free chocolate zucchini muffins are the perfect healthy way to satisfy your chocolate craving! They’re moist, fluffy and rich, but made without dairy or refined sugar.

gluten free chocolate zucchini muffins with sea salt on top

Gluten free chocolate zucchini muffins with a rich chocolate flavor but no refined sugar OR dairy?! Sounds too good to be true, but it’s not! These muffins are light yet rich, with a moist and tender crumb and beautifully domed muffin tops.

We’ll be using a few key ingredients to keep these muffins delicious but also healthy too! For dry ingredients, you’ll need oat and almond flour which keep these gluten free, plus cocoa powder for a rich chocolate flavor.

For wet ingredients, we’ll be using maple syrup and coconut sugar to sweeten, plus coconut oil and almond butter to keep them moist.

We’ll finish them off with some eggs and non-dairy milk to give them structure and nice rise! If you like this recipe, be sure to try my gluten free blueberry muffins or gluten free blueberry zucchini muffins next!

ingredients in bowls with labels

How to make gluten free chocolate zucchini muffins

GRATE ZUCCHINI. Line a muffin tray with 12 liners and set aside. Grate the zucchini and set aside. Don’t squeeze out the liquid, it will help add moisture to the muffins!

WHISK WET. Whisk together all wet ingredients until smooth.

WHISK DRY. Whisk in the dry ingredients, aside from the chocolate chips, making sure to spoon and level the flour and cocoa. Fold in the zucchini and chocolate chips.

SCOOP. Scoop the batter into the muffin tray, filling each pretty close to the top for nice round muffin tops. Add some extra chocolate chips on top.

BAKE. Bake for 5 minutes at 425, then decrease the temperature to 350 and bake an additional 14-18 minutes or until a toothpick comes out clean with a few moist crumbs. Mine are usually good at 15, but all ovens are different.

SERVE. Let cool in the tray for about 10 minutes, then remove and let finish cooling on a cooling rack.

whisking the batter together

Should I peel zucchini?

You can! But you definitely don’t have to. Since these zucchini muffins have chocolate in them, you won’t even notice the green specks, so safe yourself some trouble and just grate the zucchini as is!

A lot of recipes for zucchini bread and muffins will tell you to squeeze the extra liquid out of the zucchini, but I actually never do this!

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I like to keep the zucchini as is, since that extra moisture keeps the muffins moist and fluffy.

two images showing how to make the recipe

How to store

These gluten free chocolate zucchini muffins will keep for about 3-5 days at room temperature. I suggest keeping them in a ziplock bag or air tight container so they don’t dry out.

I like to pop one in the microwave for a few seconds so they get nice and warm and fudgy! Almost like a brownie in muffin form.

You can also freeze these after baking. Let them cool completely, then transfer to a freezer safe bag and freeze for up to 1 month. Let thaw in the fridge, then warm up in the microwave.

gluten free chocolate zucchini muffin cut in half to show texture

Ingredient substitutions

Eggs. This recipe calls for two eggs, which is just within my limit for being able to safely swap for an egg replacer. For this recipe, I would recommend mashed banana, apple sauce or flax eggs.

If you use mashed banana or apple sauce, you’ll want about 4 tbsp per egg, so 1/2 cup for the recipe, of whichever you choose. For the flax eggs, just whisk together 2 tbsp of ground flax with 5 tbsp of water, let thicken and use that in place of the two eggs.

Nut butter. I’m a *big* almond butter fan. I use it a lot! You can absolutely swap the almond butter for any other nut or seed butter of your choice such as peanut or even tahini.

For best results, use a natural one with the nut as the only ingredient.

Butter. I like using real butter because it has a rich flavor, but you can use coconut oil or a dairy free butter instead. If you use coconut oil, just make sure it is refined so there is no coconut flavor.

Flour. For these gluten free zucchini muffins, you need 1 cup each of almond and oat flour. If you want to use all of one of them, you can most likely swap 1:1 with no issues. Just make sure you’re using a total of 2 cups of flour.

Oat flour absorbs more moisture than almond flour, so if you use all almond flour, the bake time may be a little longer, so keep an eye on the oven!

one bite taken out of the gluten free chocolate zucchini muffin

Try these next!

  • Chocolate Banana Muffins
  • Sweet Potato Muffins
  • Bakery Style Chocolate Chip Muffins
  • Almond Flour Banana Muffins

Lastly, if you want more recipes straight to your inbox, be sure to subscribe to my email list. As always, tag me on instagram if you make this recipe so I can see your creation!

5 from 12 votes

Gluten Free Chocolate Zucchini Muffins

by: claire cary

These gluten free zucchini muffins are the perfect healthy way to satisfy your chocolate craving! They’re moist, fluffy and rich, but made without dairy or refined sugar.
/ /
Prep: 15 minutes mins
Cook: 20 minutes mins
Total: 35 minutes mins
12

Equipment

  • Muffin tin

Ingredients

Wet

  • 2 large eggs
  • 6 tablespoons maple syrup
  • ⅓ cup granulated sugar of choice brown, coconut, white etc.
  • 5 tablespoons butter or coconut oil melted
  • ½ cup runny almond butter or other nut/seed butter
  • 6 tablespoons milk 6 tbsp = 1/4 cup + 2 tbsp
  • 1 teaspoon vanilla extract
  • 1 teaspoon vinegar

Dry

  • 1 cup blanched almond flour
  • 1 cup oat flour
  • ½ cup cocoa powder
  • ½ teaspoon baking soda
  • 1 teaspoon baking powder
  • ¼ teaspoon salt

Mix ins

  • ½ cup chocolate chips
  • 1 cup grated zucchini with or without skin, about 1 small zucchini
US Customary – Metric

Instructions

  • Preheat the oven to 425 degrees Fahrenheit.
  • Line a muffin tray with 12 liners and set aside. Grate the zucchini and set aside. Don’t squeeze out the liquid.
  • Whisk together all wet ingredients.
  • Whisk in the dry ingredients making sure to spoon and level the flour and cocoa powder.
  • Fold in the zucchini and chocolate chips.
  • Scoop the batter into the muffin tray, filling each pretty close to the top for nice round muffin tops. Add some extra chocolate chips on top.
  • Bake for 5 minutes at 425, then decrease the temperature to 350 and bake an additional 14-18 minutes or until a toothpick comes out clean with a few moist crumbs. Mine are usually good at 15, but all ovens are different.!
  • Let cool in the tray for about 10 minutes, then remove and let finish cooling on a cooling rack.

Notes

I have not tested this recipe without eggs, but if you want to make these vegan, I would suggest apple sauce or mashed banana (about 4 tbsp per egg, so 1/2 cup for the recipe) or flax eggs. 
If using coconut oil over butter, be sure to used refined coconut oil, not virgin, to prevent any coconut flavor. 
You can use dairy or non-dairy milk here. 
Serving: 1muffin / Calories: 288kcal / Carbohydrates: 25g / Protein: 8g / Fat: 18g / Fiber: 4g / Sugar: 13g

Did you make this?

Mention @eatwithclarity or tag #eatwithclarity!

Related posts:

  1. Banana Oatmeal Breakfast Cookies
  2. Gluten Free Chocolate Banana Muffins
  3. Gluten Free Chocolate Chip Muffins
  4. Chocolate Protein Pudding
5 from 12 votes (3 ratings without comment)

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Comments

  1. Brittany
    August 21, 2025

    The GOAT of all zucchini muffins!! I wish I would have found this recipe earlier this summer (although maybe itโ€™s for the best๐Ÿคช). Catch me making these muffins every week from here on out. Used recipe as is with no subs. You have to try!5 stars

    Reply
    1. Claire Cary
      August 22, 2025

      Thanks so much, Brittany!

      Reply
  2. Stephanie
    July 22, 2025

    Honestly thought this recipe was just fun to make when I had a few free minutes this morning. I didn’t have seed or nut butters aside from peanut butter, so oh well, a little extra flavor and protein. That aside this recipe is so easy to follow and the muffins are delicious!! Will be making these again and again.5 stars

    Reply
    1. Claire Cary
      July 23, 2025

      Thank you, Stephanie! So glad you loved it.

      Reply
  3. Deanna
    May 13, 2025

    Can I sub almond flour? If so how?
    Thank you

    Reply
    1. Claire Cary
      May 14, 2025

      As in you want to replace the almond flour with something else? You can try oat flour!

      Reply
  4. Sarah
    April 1, 2025

    My husband, son and I enjoyed these muffins! They were moist and delicious! Thank you for the recipe!5 stars

    Reply
  5. Cayley
    April 1, 2024

    Okay TRUE confession… I am absolutely OBSESSED with this recipe. I am usually a recipe tweaker by nature โ€ฆ but this was perfection (Iโ€™ve make these muffins at least 7 times in the last couple of months)! Thank you so much for creating this!5 stars

    Reply
    1. Claire Cary
      April 2, 2024

      Makes me so happy! Thanks, Cayley!

      Reply
  6. Tatiana
    September 8, 2023

    Wondering how the oat flour and almond flour were measured before I try this recipe! Did you pack both flours or gently spoon into the measuring cup?

    Reply
    1. Claire Cary
      September 9, 2023

      Always spoon and level, never pack flour!

      Reply
  7. Erika
    January 24, 2023

    This recipe is fantastic! I used coconut milk as my dairy free milk alternative and used a 1/4 mixed seed butter plus 1/4 hazelnut spread for the nut butter. It is so fluffy and delicious. Thank you5 stars

    Reply
  8. Weezee
    January 16, 2023

    The batter was so thick! I had to add more milkโ€ฆ fingers crossed ๐Ÿคž๐Ÿป
    It wouldโ€™ve been helpful to add in the wet ingredients not to add the zucchini in the batter right awayโ€ฆ I messed that up

    Reply
    1. Claire Cary
      January 16, 2023

      The batter should be fairly thick, it will ensure the muffins are nice and tall!

      Reply
  9. Danyelle
    October 27, 2022

    I made these last night and oh my goodness!! They are so soft and fluffy with amazing chocolate flavor. I will definitely be making more! Thank you so much for the recipe.5 stars

    Reply
  10. Kellie Palumbo
    September 21, 2022

    Can I sub the almond flour for oat flour?5 stars

    Reply
    1. Claire Cary
      September 21, 2022

      That should be fine, but the muffins might not be quite as moist as they are with almond flour.

      Reply
  11. Kate
    April 30, 2022

    Beautiful muffins, very moist and a lovely texture. I had to sub oat flour for buckwheat flour as I didnโ€™t have gluten free oats at home and it worked superbly. My kids had no idea that there is zucchini in it! Cashew butter worked well as a nut butter. Excellent instructions, very easy to read and follow. Iโ€™m looking forward to trying out some of your other recipes. Thank you for sharing this wonderful dairy and gluten free recipe.5 stars

    Reply
    1. Claire Cary
      May 2, 2022

      Thank you Kate! I’m so glad the buckwheat flour worked well. Can’t wait to see what else you make!

      Reply
    2. Kim
      August 28, 2022

      Good call on the buckwheat flour! I had some to use up, so it saved me from blitzing some oats.
      This recipe turned out great, but I think I overbaked them by 2 minutes, as they are a wee bit dry Fantastic crackle top and great rise!5 stars

      Reply
  12. cheyenne
    August 17, 2021

    Have you tried without any nut butters at all? We aren’t super nutty fans wondering if I can omit all together or substitute something different?

    Reply
    1. Claire Cary
      August 18, 2021

      I haven’t tried it without nut butter, you can try subbing with oil and using half the amount of what the nut butter calls for. You can try sunflower seed butter or cashew butter which has a bit more of a mild flavor!

      Reply
claire cary

Welcome,
I’m Claire

Eat With Clarity is a place for gluten free recipes that are just as good as the real thing. With plenty of vegan, vegetarian and paleo options, there is something here for everyone!


Read Claire’s Story

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