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.


Comments are closed.

  • Nathaly Saucier livano
    September 20, 2020 at 2:31 AM

    Hi Nicole!
    I’m willing to try this recepy for my children lunch box tomorrow… Both have lots of intolerances which makes a big challenge to cook /bake… They can’t have nuts, milk, gluten or regular sugar (crazy that sugar makes them sick, most children get energy from it)… Could I make below replacements:
    1. Cup 4 cup blend (from your own blend as I bought all flours and have them in my pantry, I can’t find pectin to make better batter)
    2. Coconut sugar or erythritol (or mix of these) to replace sugar..
    3. Coconutmilk (from carton) + 1tbs lemon juice (to replace buttermilk). I could use also a coconut+rice drink they tolerate also really good…
    Do you think allá these swaps would work?
    Thank you so much for your support…

    • Nicole Hunn
      September 20, 2020 at 12:18 PM

      Hi, Nathaly, you can definitely use my mock Cup4Cup flour in this or any other recipe that calls for an all purpose gluten free flour. The oat flour is different. I don’t recommend using coconut sugar, as it is heavier and granier than granulated sugar. And please see the Ingredients and substitutions section for the other subs. I’m afraid that’s all the info I have!

  • Nan Stevens
    September 15, 2020 at 10:17 PM

    Since my recent celiac diagnosis, I haven’t had that much success with GF baking, but I made these muffins today and they are amazing! So moist and flavorful. Followed your recipe using butter and milk/ yogurt substitutions you recommended. Thank you for the great recipe.

    • Nicole Hunn
      September 16, 2020 at 7:31 AM

      I’m so glad you were successful, Nan! Hopefully that gave you the confidence you need to keep baking. :)

  • Valerie
    August 8, 2020 at 9:49 PM

    Great recipe!
    I made Them with gluten free flour from your site
    I hadn’t baked in so long, but the zucchini is stacking up and we’re still eating it raw. I needed a little treat! The sugar was plenty. Next time I might add vanilla and I did put in a teaspoon of cinnamon with the dried cranberries

    • Nicole Hunn
      August 9, 2020 at 6:11 AM

      Zucchini will not be ignored, Valerie! I’m glad you found this use for it. Your plans for adding some cinnamon and dried cranberries sound great.

  • EB
    August 8, 2020 at 8:27 PM

    Made this with my three year old and turned out great! I used 1/4C quinoa flour and 1/4C oat flour, added dark chocolate chips and pecans, and it was lovely! Great fluffy texture, not overly sweet, rose beautifully, and had a nice color!

    Thanks for a wonderful recipe!

    • Nicole Hunn
      August 9, 2020 at 6:11 AM

      Those are risky substitutions, Elaine. I’m glad they worked out for you. For others’ benefit, those are not all purpose gluten free flours and generally won’t work in recipes that aren’t designed for them.

  • Mary
    July 16, 2020 at 10:20 PM

    Baked these today with a freshly picked zucchini. I used quinoa flour because I did not have oat flour. I used mini chocolate chips in them. This is a wonderful tasty,moist treat!!. We’ll be making frequently. Thank you, Nicole!

    • Nicole Hunn
      July 17, 2020 at 9:59 AM

      Interesting swap, Mary. Glad it worked!!

  • Judy
    July 14, 2020 at 1:39 PM

    I made these muffins the other day and added 1/2 cup chocolate chips and the 3/4 cup of craisins. I sprinkled vanilla sugar on top the batter. They are delicious!

    • Nicole Hunn
      July 14, 2020 at 6:53 PM

      Ooooh that sounds really delicious, Judy!!

  • Margaret Cachia
    July 12, 2020 at 1:03 PM

    Hi, can i substitute buttermilk with coconut milk as I’m dairy intolerant. Thanks

    • Nicole Hunn
      July 12, 2020 at 5:45 PM

      Hi, Margaret,
      Please see the ingredients and substitutions section.

  • Cindy Ranuio
    July 12, 2020 at 12:23 PM

    I know that you have used Lakanto alternative sweetner. I am currently fighting cancer so I do not use any sugar, but I do use alternative sweetners like honey, Lakanto Monkfruit, Maple Syrup. Would I be able to substitute the sugar with one of the above in this recipe?

    • Nicole Hunn
      July 12, 2020 at 5:37 PM

      Hi, Cindy, I’m afraid you can’t substitute a liquid sweetener for a granulated one, no. You can try using Lankato monkfruit granulated sugar substitute, but it is drying so you will likely need to increase the moisture. I can’t promise success, since I haven’t tried it. I hope your health improves.

  • Bev
    July 12, 2020 at 9:58 AM

    These look delicious. I will try with dried blueberries, I think.
    Thank you for taking the time for dairy substitutions. Cow’s milk and I don’t get along, but not for the usual reasons – I get sinus infections due to the casien, which thickens mucus, as well as puddings, etc. . It took me years to discover the cause. And I grew up on a dairy farm. We thought all the sinus problems were from hay dust. (Goat milk has a different kind of casein, so I can use that, but it is costly. ) i assume coconut milk will work in this recipe.
    Keep sending the explanations and whys for doing things, like draining zucchini! I would never have thought of that for the reason my muffins go flat.

    • Nicole Hunn
      July 12, 2020 at 5:45 PM

      Dried blueberries sounds like a great choice, Bev! I would not use canned coconut milk, as it’s too thick. But you could use half coconut milk from the carton, half nondairy plain yogurt. So glad the explanation was useful!

  • Joanne
    July 12, 2020 at 9:04 AM

    Any suggestions how to make this recipe dairy free?

    • Nicole Hunn
      July 12, 2020 at 5:37 PM

      Please see the ingredients and substitutions section, Joanne.

  • Grace Zubkow
    July 8, 2020 at 9:25 AM

    Can’t wait to try these, but I’m aiming for first time success…so, is the gram weight of the zucchini determined before or after draining?

    • Nicole Hunn
      July 8, 2020 at 9:35 AM

      Good question, Grace! It would be very misleading if the gram weight was after draining for sure! The ingredient, as measured, is as is. The instructions include the draining. I try to be really precise in my recipes (the least I can do!), so I would specifically state that the weight was “as drained” otherwise.

  • Cami
    August 12, 2014 at 10:14 PM

    these look absolutely delicious! Thanks so much for sharing and I look forward to making these in the future. I plan on using the zucchini from my garden. Perfect for this recipe.

  • Lucy
    August 11, 2014 at 9:43 PM

    These look so good! Have to make these tomorrow!

  • Victoria
    August 11, 2014 at 12:46 PM

    I wish you could give us more paleo recipes!!! I know I am asking for a lot, but your recipes are so good and you are so talented that wish you would give us some more of that too :-)

    • August 11, 2014 at 3:20 PM

      Hi, Victoria, Paleo recipes seem to be of most general interest around January and February, when everyone is recovering from the holidays. Definitely look for more early next year!

  • Jennifer S.
    August 11, 2014 at 9:43 AM

    I think our kids are on the same wave length. They get cereal once a week and that’s ok but if it were more I might have a mutiny on my hands. Because we get up and go all year round (dang us working parents), I have to keep the healthy breakfast charade up all year long since I just don’t know what they are eating at the school summer program even though I packed their lunch. These will make a great addition to my muffin stash.

    P.S. I gave them cereal ONE TIME for dinner and honest to Pete you would have thought I was poisoning them.

    • August 11, 2014 at 3:14 PM

      Jennifer that is just too funny, how they reacted to your giving them cereal one time! I assume you have already tried to explain to them that most children eat cereal for breakfast most days?! I’ve tried, all to no avail, of course. ;)

  • Anneke
    August 11, 2014 at 9:20 AM

    I am right with you on the healthy breakfast, Nicole! My kids will begin freezer stocking this week, after we recover from being on vacation. These babies will join the carrot muffins at the top of list of choices, and I am sure they will have chocolate chips, cause Caroline thinks raisins taste like dirt. She’s funny like that.

    • August 11, 2014 at 3:20 PM

      Dirt, huh, Anneke? Well if she’s the one baking, then no dirt raisins. :)

      P.S. How does she know what dirt tastes like?

      • Anneke
        August 12, 2014 at 6:11 PM

        No idea, although she did eat a few unusual things as a child, so maybe dirt was in the mix.

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