Gluten Free Chocolate Zucchini Muffins (Refined Sugar Free)
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These Healthy Gluten-Free Chocolate Zucchini Muffins are dairy-free and refined sugar-free – perfect for lunchboxes, after-school snacks, or a healthy treat. They also get a little fiber and omega-3 boost from the chia seeds added in!

You all know I love my muffin recipes! I like to make healthier muffins that sneak in veggies like these Healthy Sweet Potato Zucchini Muffins (Low Sugar!) or Spinach Banana Muffins for Toddlers (No Added Sugar!).
I also love creating regular muffins that use healthier ingredients and less sugar than a typical muffin, such as these Gluten-Free Apple Muffins.
I’ve actually never created a chocolate muffin recipe before, so I’m really excited to share these Double Chocolate Zucchini Muffins today! My kids are my number one taste testers and they love them!
What You’ll Love About This Recipe
- Gluten-Free – This recipe uses almond flour, making it gluten-free and accessible to more people!
- Easy – You don’t have to squeeze and drain the water out of the zucchini!
- Gets Some Veggies In! – I love that my kids (and myself) are eating some veggies when they eat these muffins while satisfying their (let’s be real, my) sweet tooth.
Recipe Ingredients
You’ll need the following ingredients to make these Chocolate Chip Zucchini Muffins:

Ingredient Notes
- Almond Flour: I used almond flour for this recipe, but you can try a different gluten-free flour you have on hand, such as Bob’s Red Mill 1:1 Gluten-Free Flour Blend, or you can try using regular flour. I can’t speak to how these flours will perform, as I’ve only created the recipe with almond flour before! Let me know in the comments if you try out a different flour and how it works! 🙂
- Cocoa Powder: You’ll want to use unsweetened chocolate powder/cacao powder for this recipe, giving them a rich chocolate flavor. Cacao powder works great, too!
- Olive Oil: You can use coconut oil or another vegetable oil if preferred.
- Chocolate Chips: Be sure that the chocolate chips you use are gluten-free, such as Enjoy Life chocolate chips. If you want to make sure your chocolate chips are refined sugar free, Lily’s and Hu chocolate chips are good options.
Additions & Substitutions
- Walnuts: A nut like walnuts or pecans would make a nice addition to these muffins!
- Almond Flour: I’ve only made these muffins with almond flour, but you can try making them with an alternative gluten-free flour, or a regular flour if you don’t need the muffins to be gluten-free.
- Eggs: Since almond flour is pretty finicky and hard to bind, I would only make this recipe using eggs and not try to use a vegan flax egg or chia egg. If wanting to make these vegan muffins, I would recommend using a different flour that binds more easily (1:1 Gluten-Free Flour Blend or regular all-purpose flour).
- Olive Oil: You can replace the olive oil with another vegetable oil or coconut oil.
- Cocoa Powder: I’ve also made this recipe with cacao powder, and it works great!
Tools For This Recipe
How to Make Gluten-Free Chocolate Zucchini Muffins: Step-by-Step
For the full recipe with the exact ingredients, scroll down to the printable recipe card below!

Step 1: In a large bowl, mix almond flour, cocoa powder, baking powder, baking soda, salt, and chia seeds until well combined.

Step 2: In a medium bowl, combine eggs, vanilla extract, maple syrup, olive oil, and shredded zucchini. Pour wet ingredients into the flour mixture and stir to combine.

Step 3: Add chocolate chips and stir until just combined.

Step 4: Use a spoon or ice cream scoop, to scoop out muffin batter and transfer to a muffin tin lined with muffin liners. Fill each liner to the brim. Top each muffin with extra chocolate chips, if desired. Bake muffins in the oven at 350 degrees Fahrenheit for 18-20 minutes until a toothpick comes out clean when inserted into the middle of the muffin.

Recipe Tips & Tricks
- Top with nut butter – Add some more protein to your chocolate muffins by adding a dollop of almond butter (or your fav nut butter) on top when you’re ready to eat them!
- Freeze some muffins for later! – If you have extra muffins, freeze em’! Then you’ll have an easy snack ready to go later on.
- Chocolate Chips: I like Lily’s and Hu chocolate chips as refined sugar free chocolate chip options.
What to Serve With These Muffins
- Nut butter!: This will make these muffins a great snack with the extra addition of protein.
- Butter: The muffins are also delicious with a dollop of butter on them.
- Purity Coffee: My favorite clean coffee! I love their Dark Roast, Ease. Use code: SUPERMOMEATS20 for 20% off your first order.
Storage & Reheating
- Fridge: Store leftover muffins in an airtight container in the fridge for 3-4 days.
- Freezer: Let the muffins cool completely, unwrap the liners, and then transfer them to an airtight freezer-safe container or bag arranged in a single layer. Store the muffins in the freezer for up to 3 months.
- Reheating: When you’re ready to eat the muffins, reheat them in the microwave for about 30-45 seconds until heated through.

Frequently Asked Questions
I have not personally tried this recipe with any flour other than almond flour, so I can’t speak to how they’ll turn out, but you could try out a 1:1 Gluten-Free Flour Blend or regular all-purpose flour mixed with whole wheat flour (if you don’t need them to be gluten-free).
I have not personally tried to make this recipe vegan, so I can’t speak to how they’ll turn out. Since almond flour is pretty finicky and hard to bind, I would only make this recipe using eggs and not try to use a vegan flax egg or chia egg. If wanting to make these vegan muffins, I would recommend using a different flour that binds more easily (1:1 Gluten-Free Flour Blend or regular all-purpose flour).
Yep! I added the chia seeds for an extra boost of nutrients. The recipe doesn’t rely on the chia seeds.
Nope! Just throw the shredded zucchini into the mixing bowl as is. Easy peasy! 🙂

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Did you try this recipe?
Let me know how you liked it by leaving a comment and rating below! Or tag me on Instagram and share what you made!
More Muffin Recipes You’ll Love

Gluten-Free Chocolate Zucchini Muffins
Ingredients
- 2 cups almond flour, superfine and blanched
- ⅓ cup cocoa powder, unsweetened
- 1 teaspoon baking powder
- ½ teaspoon baking soda
- ½ teaspoon salt
- 2 tablespoons chia seeds
- 2 eggs
- 2 teaspoons vanilla extract
- ⅓ cup 100% pure maple syrup
- ⅓ cup olive oil, or use coconut oil or vegetable oil
- 1 cup zucchini, shredded (no need to peel zucchini or squeeze out extra moisture!)
- ¾ cup chocolate chips*, gluten-free and dairy-free if needed (plus more to top muffins with if desired)
Instructions
- Preheat oven to 350 degrees Fahrenheit. Line a muffin tin with non-stick muffin liners and set aside.
- In a large bowl, mix almond flour, cocoa powder, baking powder, baking soda, salt, and chia seeds until well combined.
- In a medium bowl, combine eggs, vanilla extract, maple syrup, olive oil, and shredded zucchini.
- Pour wet ingredients into the flour mixture and stir until just combined.
- Add chocolate chips to the muffin batter and again, stir until just combined.
- Use a cookie scoop or a spoon to scoop out muffin batter and transfer to the muffin pan. Fill each liner to the brim. Top each muffin with extra chocolate chips, if desired.
- Bake muffins for 18-20 minutes until a toothpick comes out clean when inserted into the middle of the muffin.




These were EXTREMELY delicious and easy to make. I made them two times in one week with my granddaughters three and five years old. We had so much fun and it was a great opportunity to bake together and enjoy something healthy, and delicious afterwards.
Hi Melanie! Yay! I’m so happy to hear that you and your granddaughters made these muffins together and enjoyed them! What a fun and special activity to do together. Thank you so much for taking the time to leave a rating and review! I truly appreciate it! – Kaileigh
These were a hit with my husband and my 8 year old son! I love that my family is getting a cleaner and healthier treat that has good fiber from the chia seeds, fats from almond flour, and some healthy carbs from the zucchini. These were also a great way to use up zucchini that we had because I accidentally bought too much. Also love that I didn’t have to squeeze the liquid from the zucchini.