Gluten Free Chocolate Zucchini Muffins

Gluten Free Chocolate Zucchini Muffins - soft, sweet, and decadent, made gluten free with homemade quinoa flour and almond flour!

An alternate title for this post could be, “I don’t know why it works but it does.” I can’t tell you why the zucchini-in-desserts thing works, or why these gluten free flours bake up like regular flours without the help of an egg, but they do, and I like it.

This recipe is based off of a recipe I received from my friend Terese’s mom, which may be found here. When Ryan and I had a garden a couple years ago, and more zucchini than we knew what to do with, he requested Terese’s mom’s zucchini cake. That recipe delivers in all kinds of sweet, chocolatey, crunchy-top ways. I believe we ate the entire 9×13-inch pan in about 4 days.

Gluten Free Chocolate Zucchini Muffins - soft, sweet, and decadent, made gluten free with homemade quinoa flour and almond flour!
Gluten Free Chocolate Zucchini Muffins - soft, sweet, and decadent, made gluten free with homemade quinoa flour and almond flour!

With the arrival of zucchini in our CSA box the past couple weeks, I wanted to revisit the recipe, and give it a somewhat healthier spin. I like to use whole grains in baking whenever possible, but sometimes whole wheat flour makes an otherwise awesome recipe have a little overly healthy feel, through either a denser texture or wheat-y taste. The first time I made these muffins (that are really kind of like cupcakes), I threw caution to the wind and ground up some dry quinoa to create a flour, mixed that with some almond meal, and decided to see what happened, assuming I’d have to rework it several times to account for the lack of gluten.

…but but BUT, guess what – it worked on the first try! And all the gluten free dessert lovers rejoiced, aka I did a little happy dance in my kitchen all by myself.

Gluten Free Chocolate Zucchini Muffins - soft, sweet, and decadent, made gluten free with homemade quinoa flour and almond flour!

To make sure I wasn’t just lucky with my baking endeavor, I made the recipe again, and handed a muffin to my very picky mother to try. This is a lady who wholeheartedly disagrees with vegetables in her desserts, but she actually LIKED these muffins. She told me they were good! It was a great day in my baker life.

Gluten Free Chocolate Zucchini Muffins - soft, sweet, and decadent, made gluten free with homemade quinoa flour and almond flour!

If you have a hefty amount of zucchini, I highly recommend you give these a try! They make a great mid-afternoon snack or after-dinner treat. Maybe you also want to drizzle them with melted peanut butter? You so get me.

Gluten Free Chocolate Zucchini Muffins

Gluten free chocolate zucchini muffins made with quinoa and almond flour! Soft, sweet, and vegan too!

Yield: 12 muffins

Prep Time: 15 minutes

Cook Time: 20 minutes

Total Time: 35 minutes



  • 1 cup quinoa flour (see note)
  • 1/2 cup almond flour
  • 1/2 cup cocoa powder
  • 1 teaspoon baking powder
  • 1/2 teaspoon cinnamon
  • 1/4 teaspoon fine salt
  • 1/2 cup coconut oil, melted
  • 1/2 cup granulated cane sugar
  • 1/2 cup milk of choice
  • 1 teaspoon vanilla (omit for gf, or ensure your brand is gf)
  • 1 cup shredded zucchini
  • 1/2 cup semisweet chocolate chips (vegan, if needed)


  • 2 tablespoons turbinado sugar
  • 1/4 cup chopped walnuts
  • 1/4 cup semisweet chocolate chips (vegan, if needed)


  1. Preheat oven to 400 degrees.
  2. In a medium-sized bowl, whisk together the quinoa flour, almond flour, cocoa powder, baking powder, cinnamon, and salt.
  3. In another bowl, whisk together the coconut oil and sugar, then mix in the milk and vanilla.
  4. Gradually add the dry ingredients to the wet ingredients, stirring with a fork or whisk just until incorporated. Fold in the zucchini and chocolate chips.
  5. Drop scant 1/4 cup of the batter into 12 lined and greased muffin tins.
  6. In another bowl, toss together the topping ingredients, then sprinkle on top of the 12 muffins.
  7. Bake for 20-22 minutes, until a toothpick inserted in the center comes out clean. Let sit in the tin for 5 minutes, then transfer to a cooling rack to cool completely.

Instead of buying expensive quinoa flour, I like to make my own. For this recipe, I blended 1 cup of dry quinoa in my Magic Bullet blender, but I've also had success with smaller amounts of quinoa in a coffee grinder. After blending, I measured out 1 cup of the flour (be sure to measure again, as blending 1 cup of dry quinoa will result in more than 1 cup of flour).

This recipe was tested with unsweetened almond milk, as well as whole milk. Both work great.

If you want lower sugar, feel free to reduce the amount of chocolate chips in the batter, or omit them completely and just have them on top. For me? The more chocolate the better!

Nutrition Information: Serving Size: 1 muffin, Calories: 257, Total Fat: 16.3g, Saturated Fat: 10.8g, Cholesterol: 0mg, Sodium: 63mg, Potassium: 181mg, Total Carbs: 28.0g, Dietary Fiber: 3.0g, Sugars: 17.1g, Protein: 3.0g

Gluten Free Chocolate Zucchini Muffins - soft, sweet, and decadent, made gluten free with homemade quinoa flour and almond flour!


25 Responses to “Gluten Free Chocolate Zucchini Muffins”

  1. Laura — July 21, 2015 @ 6:19 am (#)

    Looks yummy 

  2. Lauren Gaskill | Making Life Sweet — July 21, 2015 @ 9:58 am (#)

    Beautiful and delicious! I have a zucchini that is almost two feet long in the fridge right now. These are perfect for dessert this week. :)

  3. Lucie A.S — July 21, 2015 @ 10:31 am (#)

    AW-ES-OME! I can almost taste the crumbly crunchy topping with the turbinado sugar, walnuts and melt in your moth chocolate uugghh!! 
    I am craving this right now!
    Thank you for the quinoa flour tip too :) 

    Big hugs!

  4. Nicole — July 21, 2015 @ 2:01 pm (#)

    These look great.
    Just one question:
    I thought Quinoa has to be rinsed to rid it of bitter saponins.
    If I grind it without rinsing will my muffins be bitter?

    • Katie — July 21, 2015 @ 2:10 pm (#)

      Hi there! Mine were not bitter, and I did not rinse my quinoa before grinding. If you’re worried about it you could always purchase quinoa flour instead of making your own.

  5. felicia@ingredient1 — July 21, 2015 @ 4:39 pm (#)

    We had some delicious gluten-free muffins this morning from Hu Kitchen in NYC and really enjoyed them. Excited to try to make our own, and will definitely take you up on your suggestion to make our own quinoa flour! Thanks so much.

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  7. Emma — July 27, 2015 @ 7:32 pm (#)

    LOVE these photos and the small amount of sugar used. Wishing I bought zucchini yesterday at the market! 

  8. Nicoletta @sugarlovespices — July 28, 2015 @ 8:28 am (#)

    Beautiful looking muffins and super gluten-free deliciousness! I love the combo chocolate zucchini!

  9. Vicky — August 2, 2015 @ 6:07 pm (#)

    I adore this recipe not only because of the healthy flours you have chosen but also because the cakes look so awesome in your beautiful photos!

    • Katie — August 2, 2015 @ 6:59 pm (#)

      Thank you!

  10. Debbie — August 11, 2015 @ 6:10 pm (#)

    Could I substitute coconut sugar for the cane and turbinado sugar?

    • Katie — August 11, 2015 @ 10:12 pm (#)

      You definitely can for the cane sugar, but I’m not sure about the turbinado sugar – it really adds a crunch to the top. You can definitely try, but let me know how it goes!

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  12. Ashleigh — August 21, 2015 @ 3:27 pm (#)

    Can I substitute oat flour or whole wheat flour for the quinoa flour? I just have everything on hand, but that.

    • Katie — August 21, 2015 @ 3:43 pm (#)

      I’m not sure since I haven’t tried it. I would think finely-ground oat flour would be closest in taste and texture, but can’t say for sure. Let me know how it goes if you try!

  13. angela — September 2, 2015 @ 10:18 pm (#)

    Can you substitute all quinoa flour in place of the almond flour? I like to make these type of snacks for my son’s school and they can’t have any nuts/peanuts at the school. (Which obviously means no crunch toppings. That is fine – it’s extra sugar the kids don’t need anyway! :)

    • Katie — September 3, 2015 @ 8:51 am (#)

      I can’t say for certain because I haven’t tried it. You could try all quinoa flour, or maybe swap in oat flour for the almond flour. If you give it a try let me know how it goes!

  14. angela — October 3, 2015 @ 4:22 pm (#)

    I just finished making the batter. Is it suppose to be more like the consistency of cookie dough batter or muffin batter? Mine was harder and not thinned out at all like muffin batter usually is. Also, you forgot to mention when mixing dry ingredients – the cinnamon! Will see how it turns out!

    • Katie — October 3, 2015 @ 11:06 pm (#)

      It is a thicker batter than most muffins. I fixed the cinnamon issue in the instructions – thanks!

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  19. Nikki — May 15, 2016 @ 10:46 am (#)

    I just made these. DIdn’t really have milk though so I substituted an egg and a touch of the cream I put in my coffee-thus, did not accurately follow recipe. They are pretty – but a little like a brownie muffin. I would probably go with four stars. Thanks for sharing. Looking forward to trying some of your other recipes.