Almond Flour Zucchini Muffins (Gluten-Free)

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These Almond Flour Zucchini Muffins with chocolate chips and pecans are deliciously moist and tender. They’re naturally gluten-free, dairy-free and oil-free, and perfectly spiced with cinnamon, ginger and nutmeg!

I know there are definitely some skeptics when it comes to vegetables in baked goods, but I promise, you can’t taste the zucchini in these muffins!

Besides, technically, zucchini is a fruit!

Overhead view of a zucchini muffin cut in half on a parchment paper wrapper on a wire rack.

The reason I love to bake with zucchini (besides the hidden veggies) is that it adds moisture to baked goods. These chocolate zucchini cupcakes and chocolate zucchini cake are ridiculously soft and tender!

While the almond flour in this recipe keeps these muffins moist, some grated zucchini just makes them even more fluffy and tender.

Why you’ll love these almond flour zucchini muffins

Since they’re made with almond flour, they’re naturally gluten-free, and they’re also dairy-free, since we’re using plant-based alternatives.
While we’re using summer produce in this recipe, these muffins are perfectly spiced for fall. The perfect muffin for bridging the summer and fall seasons!
We’re using natural almond butter as a healthy fat in these muffins, so there is no need for added oil (and we’re not using any butter either).
These muffins are freezer friendly so they’re perfect for make ahead snacks or quick breakfasts.
There are plenty of ways to customize these muffins with recipe variations and substitutions included below.

Details on the ingredients

For a full list of the ingredients and quantities used, please refer to the recipe card at the end of this post.

Ingredients to make almond flour zucchini muffins arranged in individual dishes.

Zucchini – You’ll need 1 1/2 cups of coarsely grated zucchini for these muffins, or 155 grams. I don’t recommend finely grated zucchini as it adds too much moisture. Just use the larger shredding holes on your box grater.

Almond flour – Using finely ground blanched almond flour helps produce a tender crumb for these muffins. I normally buy the large bags at Costco, but you can also find it in the organic section of most grocery stores.

Eggs – To help give these muffins structure, you’ll need 2 large eggs

Almond butter – Since these muffins are free of oil and butter, the natural almond butter provides the much needed fat content. It also adds some protein to the muffins. To ensure the almond butter whisks together easily with the other wet ingredients, make sure it is a more pourable or drippy consistency.

Coconut sugar – This type of sugar adds a rich, caramel flavor and is less refined than brown sugar. I haven’t tested this recipe with brown sugar, so if you make the substitution, keep in mind that it may add more moisture to the muffins.

Maple syrup – For a little extra sweetness and maple flavor, the recipe also calls for maple syrup.

Almond milk – To keep these muffins dairy-free, you’ll need unsweetened almond milk. Other plant-based milks will work too. Just make sure they’re unsweetened and unflavored.

Vanilla – A flavor enhancer for most baked goods. For the best flavor, be sure to use real vanilla extract.

Salt – Also used to enhance flavor. I used fine sea salt but kosher or table salt work too.

Baking powder and baking soda – Used together for leavening.

Spices – Ground cinnamon, ginger and nutmeg make sure these muffins have a warm spiced flavor.

Chocolate chips – Mini dairy-free chocolate chips add just a touch more sweetness to these muffins.

Pecans – Some chopped raw pecans add a little crunch and texture. Make sure you use raw and not roasted or salted.

How to prepare zucchini for these muffins

Before you start making the muffins, you’ll want to grate the zucchini and squeeze the excess moisture out of it.

First, start by coarsely shredding the zucchini by using the larger shredding holes on a box grater (cheese grater). If you use the small holes and finely shred the zucchini, it may add too much moisture to the muffins.

Once the zucchini is grated, you’ll need to press or squeeze it to remove the excess moisture. You can do this by wrapping the grated zucchini in clean paper towels or in a clean tea towel and wringing it out. The zucchini should go from weighing 155 grams to about 110 grams.

How to make zucchini muffins with almond flour

Below is just a quick overview of how to make the muffins (including photos). Please check out the recipe card at the end of this post for more details.

Collage of 4 images showing how the zucchini muffins are made.

Whisk together the almond flour, spices, baking powder, baking soda and salt.

In a separate bowl, whisk together the room temperature eggs, almond butter, coconut sugar, maple syrup, almond milk and vanilla.

Once combined, stir the drained zucchini into the wet ingredients.

Add the dry ingredients to the wet mixture and stir until just combined.

Fold in the chocolate chips and pecans. (I usually reserve some for the tops but this is optional).

Divide the batter into a 12-cavity muffin pan (greased or lined with cupcake liners).

Top with remaining chocolate chips and pecans and bake for 19-21 minutes at 350F.

Let muffins cool in the pan for 10 minutes before transferring to a wire rack to cool completely.

Measuring ingredients

For convenience, US cup measurements are included in the recipe card for this recipe. To ensure greater accuracy, however, weight and volume measurements are also provided. So, if you see grams (g), you’ll want to use a kitchen scale to weigh your ingredients, and if you see milliliters (ml), you’ll want to use a liquid measuring cup. Smaller quantities of ingredients are provided in teaspoons and tablespoons.

Recipe variations and substitutions

Swap out the almond butter for natural peanut butter.
Use another plant-based milk instead of almond milk such as cashew milk.
If you don’t need the recipe to be dairy-free, you can use cow’s milk.
Use all ground cinnamon instead of a mix of spices. Chai spice or pumpkin spice would also be nice.
Instead of pecans, add raw chopped walnuts or almonds.
You can also leave out the chocolate chips if you like or add more instead of nuts.

Storage tips

These zucchini almond flour muffins are super moist, so if you’re not enjoying them within a day, I would refrigerate or freeze them. You can keep them in an airtight container at room temperature for 2-3 days, but the tops will get a little sticky from the extra moisture.

If stored in the fridge, they will last for 5-7 days.

You can also store them in the freezer for up to 3 months. Just defrost at room temperature for an hour or so before enjoying.

Zucchini muffins arranged on a wire cooling rack.

FAQs for gluten-free zucchini muffins

Do you need to squeeze the moisture out of the grated zucchini?

Yes, you definitely need to do this. Otherwise, the muffins will have too much moisture and may have a soggy texture.

Do you need to peel zucchini before baking with it?

There is no need to peel zucchini for baking. The skin is thin so it really isn’t noticeable. You’ll just want to make sure the zucchini doesn’t have any dents or blemishes on the skin, and wash it well before shredding it.

Can you make these zucchini muffins egg-free?

In order to make them egg-free, you’d need to use an egg replacement such as flax eggs. I have not tested this so I can’t say for certain if the muffins will turn out.

Can these muffins be made with all purpose flour?

As almond flour and all-purpose flour are very different, I don’t recommend substituting with all purpose flour without making other changes to the recipe.

Are these almond flour zucchini muffins low carb?

Each muffin contains 20 grams of carbs so I would not consider them low carb.

Key recipe tips

Zucchini. When you squeeze the moisture from the grated zucchini it should reduce from 155 grams to about 110 grams.
Almond butter. You’ll want to use almond butter with a running consistency. If it has hardened in the fridge, just microwave the amount you need for 10-15 seconds or until it is pourable. This will make it easier to mix in with the other wet ingredients.
Measuring ingredients. If you don’t have a kitchen scale to weigh your almond flour and sugar, be sure to measure it using the spoon and level method with a dry measuring cup. The grated zucchini should be loosely packed in a measuring cup.
Muffin pans. Darker colored pans will brown muffins more quickly than lighter colored pans. These muffins were baked in a lighter colored pan, so if your pan is dark, your muffins may bake faster.
Muffin liners. I like to use parchment paper liners as they don’t stick to the bottom of muffins like other liners do. If you don’t have liners, you can use non-stick cooking spray to grease your muffin pan.

Zucchini muffins topped with chocolate chips and pecans and cooling on a wire rack.

More almond flour recipes

More muffin recipes

If you make this recipe, I’d love to hear what you think in the comments below!

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