These Gluten-Free Chocolate Zucchini Muffins are a delicious treat for kids and adults and are a great way to get some veggies in! They also have a nutrition boost from the chia seeds added in. I hope you love the chocolatey goodness of these gluten free muffins!

A Gluten-Free Chocolate Zucchini Muffin with a bite out of it.

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!) or regular muffins that just use healthier ingredients and less sugar than a typical muffin such as Healthy Blender Banana Blueberry Oatmeal Muffins.

I’ve actually never created a chocolate muffin recipe before, so I’m really excited to share these Double Chocolate Zucchini Muffins today!

What You’ll Love About This Recipe

  • Gluten-Free – This recipe uses almond flour, making it gluten-free and accessible to more people!
  • Easy –  Combine dry ingredients, then wet ingredients, and bake in the oven for 18-20 minutes.
  • Gets Some Veggies In! –  I love that my kids (and myself) are eating some veggies when they eat these double chocolate 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.
  • 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.

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: Mix Dry Ingredients

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

STEP 2: Mix Wet Ingredients

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.

Dry ingredients in a bowl.
Wet ingredients in a bowl.

STEP 3: Add Chocolate Chips

Add chocolate chips and stir until just combined.

STEP 4: Bake

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.

Muffin batter in a bowl.
Muffin batter with chocolate chips in a bowl.

Recipe Tips & Tricks

  • Top with nut butter – Add some more protein to your healthy chocolate muffin by adding a dollop of almond butter (or your fav) on top when you’re ready to eat them!
  • Freeze some muffins for later! – If you have extra muffins that you don’t think you’ll get to, freeze em’! Then you’ll have an easy snack ready to go later on.

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.
A muffin sitting on a muffin liner.

Additions & Substitutions

Additions:

  • Walnuts: A nut like walnuts or pecans would make a nice addition to these muffins!

Substitutions:

  • 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.

What to Serve With Healthy Chocolate Zucchini 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.
A chocolate zucchini muffin with a bite out of it.

Frequently Asked Questions

Can I use a different type of flour?

I have not personally tried this recipe with any other flour 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).

Can I make these muffins vegan?

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).

Will this recipe work if I omit the chia seeds?

Yep! I added the chia seeds for an extra boost of nutrients. The recipe doesn’t rely on the chia seeds.

Do I need to strain the excess moisture from the zucchini?

Nope! Just throw the shredded zucchini into the mixing bowl as is. Easy peasy! 🙂

Tools For This Recipe

I hope you love these Gluten Free Chocolate Zucchini Muffins! If you make them, be sure to leave a rating below so I know how you liked it! Enjoy!

A Gluten-Free Chocolate Zucchini Muffin with a bite out of it.
5 stars (1 rating)

Gluten-Free Chocolate Zucchini Muffins

Yield: 12 muffins
These Gluten-Free Chocolate Zucchini Muffins are a delicious treat for kids and adults and are a great way to get some veggies in!
Prep Time: 10 minutes
Cook Time: 20 minutes
Total Time: 30 minutes

Ingredients
 

  • 2 cups almond flour, superfine and blanched
  • 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
  • cup 100% pure maple syrup
  • 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 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 spoon or ice cream scoop, to scoop out muffin batter and transfer to the muffin tin. 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.
Course: Snack
Cuisine: American
Diet: Gluten Free
Calories: 268kcal, Carbohydrates: 20g, Protein: 6g, Fat: 20g, Saturated Fat: 4g, Polyunsaturated Fat: 1g, Monounsaturated Fat: 5g, Trans Fat: 0.01g, Cholesterol: 27mg, Sodium: 191mg, Potassium: 135mg, Fiber: 4g, Sugar: 13g, Vitamin A: 61IU, Vitamin C: 2mg, Calcium: 98mg, Iron: 1mg
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