These are the best paleo zucchini muffins with chocolate! Tender and moist on the inside and loaded with chocolate they are made with almond flour, coconut flour and tapioca flour. They are really easy to make and also gluten free and dairy free! Perfect for breakfast, snacks or anytime.

Why you will love this recipe:
- These are the absolute best paleo zucchini muffins! They have the most amazing crisp muffin tops yet are nice and moist on the inside. Just like a bakery style muffin.
- They are loaded with chocolate. And who doesn’t love chocolate? It makes these muffins even more indulgent.
- They are really easy to make and you don’t have to squeeze the liquid out of the zucchini, making them even easier!
- These muffins freeze really well and make a great breakfast, snack or dessert.
- They are made in one bowl and are great for meal prep.
- Besides being paleo, these zucchini muffins are also grain free, gluten free, dairy free and refined sugar free.
Ingredients and substitutions:
- Almond flour – this is one of my favourite grain free flours! You could swap this for cashew flour.
- Tapioca flour – this helps give the muffins such a light and fluffy texture. I don’t recommend swapping this for another flour.
- Coconut flour – this helps add just the perfect amount of crunch to the muffin top. I don’t recommend swapping this for another flour.
- Coconut sugar – My favourite natural granulated sugar that adds the perfect amount of sweetness to these muffins.
- Coconut oil – to help keep the muffins nice and moist.
- Baking soda – to help them rise and give these muffins the perfect texture . I recommend using aluminum free baking soda.
- Sea salt – this helps enhance the other flavours in these muffins.
- Eggs – to help these muffins rise and retain their moisture.
- Full fat coconut milk – to give these muffins some healthy fats and even more moisture. You could swap this for another dairy free milk such as almond milk or cashew milk.
- Fresh zucchini– the star of these muffins! You are going to love that you don’t have to squeeze the zucchini to make these muffins.
- Dairy free and soy free chocolate bars – My favourites are Hu Kitchen and Zazubean. You could easily use dairy free chocolate chips instead.

How to make this recipe:
You are going to love how easy these muffins are to make!
Step one:
First, preheat your oven to 350 degrees Fahrenheit.
Step two:
Then add all the ingredients, except for the chocolate, to a large bowl and stir well until smooth. Then stir in the broken chocolate pieces.
Step three:
Next, line a muffin tray with parchment paper muffin cups and fill each muffin cup until it’s heaping (see the photo).
Step four:
Lastly, bake the muffins for ~25 minutes, until the tops are golden and a toothpick inserted inside comes out clean.

Chef’s tips:
- Do not try swapping the flours! I have not tested this recipe with any other flour combinations and don’t suspect they will work out if you make your own substitutions.
- I always recommend lining your muffin tray with parchment paper muffin liners. This ensures your food will not come into contact with the non-stick coating on the tray (which is associated with many different health problems – read more about that here) and also makes the clean up so simple!
- You do not need to squeeze the liquid out of the zucchini before making these muffins.
- These muffins freeze really well so feel free to make a double or triple batch and save some for later.
Variations and add ins:
- Instead of broken chocolate bars you can use dairy free chocolate chips instead – these are my favourite chocolate chips that are sweetened with coconut sugar.
- Feel free to add other additions such as raisins or chopped nuts.
How to store:
Store these muffins in an air tight container in the fridge for up to 7 days after you make them.
Frequently asked questions:
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.
Are these AIP zucchini muffins?
This is not an AIP muffin recipe as it uses almond flour which is not allowed on the AIP diet.
Other paleo baked goods you will love:
- The Best Paleo Bread
- Paleo Orange Chocolate Chunk Muffins
- Paleo Chocolate Chip Banana Bread
- Paleo Biscuits
- Paleo Lemon Blueberry Muffins
- Vegan Peach Cobbler
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Paleo Zucchini Muffins with Chocolate
These are the best paleo zucchini muffins! Loaded with chocolate, they have the perfect bakery style muffins texture so you would never know that they are gluten free, grain free and dairy free!
Ingredients
- 2 1/2 cups almond flour
- 1/2 cup tapioca flour
- 1/2 cup coconut sugar
- 2 tbsp coconut flour
- 1 tsp 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 tsp organic vanilla extract
- 2 chocolate bars, broken into pieces
Instructions
-
Preheat your oven to 350F.
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In a large bowl mix all the dry and the wet ingredients, except for the chocolate, and stir well until smooth.
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Add in the chocolate pieces and stir in until smooth.
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Line a muffin tray with large parchment 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!
Recipe 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.
- These muffins freeze really well.
- Nutritional values are an estimate and will vary depending on the specific ingredients used. Â
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Such a delicious treat!