Gluten Free Zucchini Muffins | On the Healthy Side

Gluten Free Zucchini Muffins | On the Healthy Side

These tender gluten free zucchini muffins are made with healthy fats and some whole grains, and they’re relatively low sugar. Add chocolate chips, raisins, or chopped nuts.

Baked zucchini muffins in muffin tin

These muffins are healthy-ish

Moist, tender, only lightly sweet and still really flavorful, these gluten free zucchini muffins are healthier than most, but definitely not “diet” muffins. They’re made with a combination of an all purpose gluten free flour blend and whole grain oat flour, and of course tons of zucchini (insert zucchini emoji here why isn’t there one?).

There’s only half a cup of sugar in the whole dozen+ batch of generously-sized muffins. I used to make them with raisins all the time, but I’ve transitioned to using chocolate chips almost exclusively. There aren’t that many mix-ins and for the love of Mike even just a few chocolate chips are so good in muffins.

Zucchini muffin batter in muffin wells

Tips to making these muffins

I’ve also switched to making about 12 muffins from making nearly double that with the same amount of muffin batter. I just love a muffin with a true muffin top, so I now fill those muffin cups all the way to the top.

Filling the wells to the top, you may get 12 muffins or you may get more. It will depend on the size of the wells in your muffin tin.

I’m pretty sure I’m the only one in my family who cares about the beauty of the muffins at all. But a muffin top has a slightly crisp texture around the edges that a muffin without a true top simply doesn’t.

Whole baked zucchini muffins on a tray

Draining the zucchini

The batter mixes up very easily. You do have to squeeze as much water out of the zucchini as possible or you’ll end up with batter that’s way too wet.

A kitchen towel with a flat weave (a tea towel) works fine, but a fine mesh bag works even better. I have a nut milk bag that has dedicated its life to draining my zucchini.

Why drain zucchini in the first place, you ask?

Some recipes are formulated to be made with zucchini that hasn’t been drained of excess moisture, but zucchini vary a ton in their moisture content from one to the next. That makes it very difficult to control for the amount of moisture in your zucchini versus my zucchini. Or even in two of my very own zucchini.

Never attempt to bake with one of those enormous zucchini that you left for a day too long in the garden during the hottest days of the year. If your zucchini has been left to grow for too long, past a certain point of growth it’s just gaining water. 

Even if you’re baking with appropriately-sized zucchini, there is a fair amount of variation in moisture content. By squeezing the water out of your grated zucchini, we’re controlling for that.

A muffin batter that has too much water will expand quickly in the oven. The muffins would look puffy when they’re just baked, but they’d sink in the middle as they cooled and before we know it, you’re commenting on this post that the recipe is terrible. ?

Two zucchini muffins each on a small white plate

Ingredients and substitutions


These muffins aren’t made with butter, so there’s no need to replace the fat. But if you can’t have dairy, you’ll need to replace the buttermilk.

My favorite way to replace buttermilk is half plain yogurt, half milk. If you can have dairy, you can use dairy ingredients. If not, use nondairy plain yogurt and unsweetened plain nondairy milk, like almond milk.

Coconut oil

The virgin coconut oil that’s called for in this recipe is the jarred kind that’s solid at room temperature. Well, in the middle of the summer in my house, it tends to be kind of a liquid—but you know what I mean.

If you don’t have coconut oil, you can use vegan butter or even unsalted butter in its place. Nearly any fat that is mostly solid at room temperature should work.


There are a lot of eggs in this recipe, so I don’t recommend replacing them with an egg replacer. With this many eggs, you really need a different recipe. So sorry!

Oat flour

I never buy oat flour, but I bake with it all the time by grinding my own oat flour in a blender. If you can’t have oats, although certified gluten free oats are safe on a gluten free diet, try replacing the oat flour in this recipe with quinoa flakes.


Zucchini muffin cut in half on a plate

Zucchini muffins raw in a pan, baked in a pan, cut in half and whole on a trayHealthy Gluten Free Zucchini Muffins

Like this recipe?

Prep time: Cook time: Yield: 12 to 14 muffins


3 1/4 cups (about 300 g) grated fresh zucchini

1 1/2 cups (210 g) all purpose gluten free flour (I used Better Batter)

3/4 teaspoon xanthan gum (omit if your blend already contains it)

2/3 cup (80 g) certified gluten free oat flour

1 teaspoon baking soda

1 1/2 teaspoons baking powder

1/2 teaspoon kosher salt

1/2 cup (100 g) granulated sugar

1/2 cup (112 g) virgin coconut oil, melted and cooled

4 eggs (200 g, weighed out of shell) at room temperature, beaten

1/2 cup (4 fluid ounces) buttermilk, at room temperature

1 cup (100 g)  raisins, chopped nuts, chocolate chips or another small dried fruit


  • Preheat your oven to 350°F. Grease a standard 12-cup muffin tin and set it aside.

  • Drain the zucchini. Place the grated zucchini in the center of a large clean tea towel (a kitchen towel with a flat weave) or in a fine mesh bag, gather the towel around the zucchini, and twist tightly to squeeze out as much liquid as possible. It should reduce in weight by nearly half. Set the zucchini aside.

  • In a large bowl, place the all purpose flour, xanthan gum, oat flour, baking soda, baking powder, salt, and sugar, and whisk to combine well. Add the grated zucchini and mix to combine, breaking up any clumps. Create a well in the center of the dry ingredients and add the coconut oil, eggs, and buttermilk, and mix to combine. The batter will be thick but not stiff. Add the chocolate chips, raisins or chopped nuts, and mix until they are evenly distributed throughout the batter.

  • Fill the prepared wells of the muffin tins about completely full with batter. With wet fingers, smooth the tops of the batter in the wells and place them in the center of the preheated oven. Bake for about 20 minutes, or until the tops of the muffins spring back when pressed gently and a toothpick inserted in the center comes out mostly clean, or with a few moist crumbs attached. Remove from the oven and allow to cool for at least 5 minutes before transferring to a wire rack to cool completely. If you have any leftover batter, repeat with whatever remains.

  • These muffins freeze very well in a freezer-safe container. Just eliminate as much air as possible from the container before freezing the muffins in a single layer, and defrost on the counter overnight before serving. They can be refreshed in the toaster oven before serving.

  • Originally published on the blog in 2014. Sugar changed from brown to granulated; muffin size increased. Photos and video new.


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