These are the best gluten-free chocolate chip zucchini muffins! Not only do they taste amazing but they are really easy to make and these healthy muffins are made with almond flour and coconut flour and are also dairy-free, paleo, and refined sugar free.

Healthy muffins like my gluten-free banana chocolate chip muffins, chocolate avocado muffins and gluten-free lemon blueberry muffins are some of my favourite recipes to create, and the chocolate zucchini muffins I am sharing with you today are my latest muffin obsession!
Table of Contents
Why you will love these muffins:
- The taste! These are the absolute best gluten-free zucchini muffins! They have perfectly firm muffin tops yet are nice and moist on the inside and are bursting with chocolate chips.
- They are really easy to make and you don't have to squeeze the liquid out of the zucchini. They are also made in just one bowl so the clean up is really quick.
- Besides being gluten-free, these healthy zucchini muffins are also grain-free, paleo, dairy-free and refined sugar free.
If you love baking with zucchini you will also love my healthy double chocolate zucchini bread!
Ingredients:
For the exact measurements refer to the recipe card later in this post.
Jump to the Recipe Card.- Dry ingredients: almond flour, tapioca flour or tapioca starch, coconut flour, baking soda and salt. Be sure to use almond flour and not almond meal which is more gritty.
- Wet ingredients: coconut oil, full fat coconut milk, and vanilla extract.
- Sweetener: coconut sugar adds the perfect amount of sweetness to these muffins while keeping them refined sugar free.
- Eggs: these help the muffins rise when they bake and help the muffins stay together and prevent them from being too crumbly.
- Fresh zucchini - this adds tons of moisture to these muffins plus a nice serving of veggies.
- Dark chocolate chips - instead of chocolate chips you can also use chocolate chunks or broken chocolate bars.
Recipe variations and add ins:
- Feel free to add other ingredients such as raisins or chopped nuts like pecans or walnuts.
- You could swap the almond flour for cashew flour.
- Instead of coconut milk you could use another milk such as almond milk or cashew milk.
How to make gluten-free chocolate chip zucchini muffins:
- Step 1: Preheat your oven to 350 degrees Fahrenheit and add all the ingredients, except the chocolate chips, to the bowl of your standing mixer.
- Step 2: Blend the ingredients until you have a smooth batter.
- Step 3: Stir in the chocolate chips by hand.
- Step 4: Line a muffin tray with parchment paper muffin cups and fill each muffin cup with the batter. Bake the muffins for 25 minutes, until a toothpick inserted inside comes out clean.
Top Tips:
- Do not try swapping the flours! I can't guarantee that any swaps will work out.
- You don't need to peel the zucchini before you grate it.
- Use room temperature eggs for best results.
- To keep these muffins refined sugar free: use chocolate chips sweetened with coconut sugar.
- Use parchment paper muffin cups to make the muffins easier to remove from the pan.
Gluten-free chocolate chip zucchini muffins FAQs:
No! They will not turn out. Cassava flour and tapioca flour are totally different flours and cannot be used interchangeably.
If you can't have almond flour I would recommend cashew flour instead.
I have not tested this recipe without eggs myself, but have had a few readers try both chia seed and flax seed eggs with success.
Store these muffins in an airtight container in the fridge for up to 7 days. These muffins also freeze really well in an airtight bag or container for up to 3 months.
I have not tried omitting the eggs from the recipe to make these muffins vegan. I have had a few readers try both chia seed and flax seed eggs and they apparently worked well but I have not tried this myself so can't guarantee the results.
Other gluten-free baked goods you will love:
Recipe
Gluten-free Chocolate Chip Zucchini Muffins
Ingredients
- 2 1/2 cups almond flour
- 1/2 cup tapioca flour
- 1/2 cup coconut sugar
- 2 tablespoon coconut flour
- 1 teaspoon baking soda
- pinch sea salt
- 3 large eggs
- 1 cup grated zucchini
- 1/2 cup full fat coconut milk
- 1/4 cup melted coconut oil
- 1 teaspoon organic vanilla extract
- 1 cup chocolate chips
Instructions
- Preheat your oven to 350F.
- Add all the ingredients, except for the chocolate chips, to the bowl of your standing mixture and blend everything well until you have a smooth batter.
- Stir in the chocolate chips by hand.
- Line a muffin tray with large parchment paper muffin cups and fill each cup with batter until it is full, and slightly heaping.
- Place the tray in the oven and bake for 25 minutes, until the muffins are golden brown and a toothpick inserted inside comes out clean.
- Let them cool and enjoy!
Notes
- This recipe yields 12 muffins.
- Do not try swapping flours, this recipe has not been tested with any other grain or gluten-free flours and I cannot guarantee that any swaps would work.
- Nutritional values are an estimate and will vary depending on the specific ingredients used.
Lori
My husband loved these; which is great!! I love that you don’t need to squeeze the zuchinni!! Thank you! Great texture, moistness. I did t add enough chocolate chips, but that was still ok!!
Erin Carter
I'm so glad you liked them!
Kristie
Such a delicious treat!