Last Updated on March 26, 2022 by Anne-Marie

Make this gluten-free zucchini muffins recipe when you’re overwhelmed with too much zucchini in your garden.

Why this recipe works

My kids LOVE these healthy zucchini muffins. It’s a nice way to sneak some veggies into their diets, too.

These are super moist thanks to all the grated zucchini. Plus, the cinnamon and spices make these muffins oh so delicious. You’d never know they’re gluten-free!

How to make gluten-free zucchini muffins

First, preheat your oven. Super important!

Preparing the muffin tins: Line a couple of muffin tins with 12 to 18 paper liners. I use paper liners because they prevent the muffins from sticking. Plus they look nice.

Making the batter: In a large mixing bowl, whisk together all the dry ingredients.

Place the raisins in a small bowl, and sprinkle them a bit of the dry mixture. This will prevent the raisins from sinking to the bottom of the muffins while they bake.

In another small bowl, whisk your wet ingredients together.

Now add the wet ingredients to the dry ingredients and mix until just combined. Don’t over stir.

Finally, stir the shredded zucchini and raisins into the big mixing bowl. Again, don’t over stir. It’s OK if there are a few streaks of flour left.

Making the muffins: Divide the muffin batter evenly among the 12 to 18 muffin cups.

Bake for 12 to 15 minutes or until a toothpick or cake tester inserted in the middle comes out clean.

Let the muffins cool for 5 minutes in the muffin tins before placing them on a baking rack to finish cooling.

Store: In a large airtight container or Ziploc baggies.

Tools needed to make zucchini bread muffins

● Muffin tins – there are traditional metal muffin tins and silicone muffin tins. You can use 6-cup or 12-cup muffin tin.

The nice thing about silicone is that you don’t need to use liners (just a little cooking spray).

Instead, you just pop out the muffins after they cool. (Just remember to place them on a baking sheet. They’re kind of floppy.)

● Cupcake liners – You can use either cupcake paper liners or silicone cupcake liners for your muffins.

If you use paper liners and don’t like the zucchini muffin showing through, bake the muffin in one liner. Then after it cools add another liner.

I like using a plain one to bake in and a colorful patterned one on the outside.

You can see how I use this effect in my Gluten Free Chocolate Bacon Cupcakes Recipe. So pretty!

● Mixing bowls – Do you have a favorite set of mixing bowls? I wish I still had my mom’s vintage Pyrex bowls from the ‘60s!

● Shredding – Sure you can use a box shredder to grate the zucchini, but that’s soooo much work and difficult if you have issues with your hands.

I prefer using a food processor since it’s quick and easy, and captures all the moisture from the zucchini.

Here’s a list of the best food processors on Amazon. (I have a Cuisinart food processor, which I love!)

● Wilton Batter Spoons – Now that I use these batter spoons my muffins and cupcakes come out more uniformly in size.

● Wilton Bake It Better Cake Tester – I prefer using a cake tester instead of toothpicks to determine if muffins are done. Toothpicks leave a bigger hole.

I love this cake tester since it’s stored in a case, which makes it easier to find in my gadget drawer.

● Baking rack – Invest in a few baking racks to cool your muffins on.

Making gluten-free muffins

If you want to make gluten-free muffins, for the best results, use Bob's Red Mill Gluten-Free 1-to-1 Baking Flour. This is my favorite gluten-free all-purpose flour.

This type of gluten-free flour blend has white rice flour, xanthan gum, potato starch, etc. so it bakes up just right and you don’t have to buy extra specialty ingredients.

(Learn how to measure flour correctly for the best results in your everyday baking.)

Check out my Best Gluten Free Products List to find more terrific gluten free baking products!

Tips for making easy zucchini muffins

Tips for preparing the zucchini: There’s no need to peel the fresh zucchini before shredding. Just wash and cut off the ends in this zucchini recipe.

Also, don’t pat the zucchini dry with a paper towel or squeeze out the liquid. You want all that precious moisture. Otherwise, you’ll end up with dry muffins.

If you feel there’s excess moisture, you can add an extra tablespoon of flour.

Make prettier muffins: If you wish, you can top the muffins with a little sprinkle of decorative sugar before baking for added sparkle just like they do at the bakery.

Using decorative sugar does add some extra calories, but I think it’s worth it.

Can I freeze zucchini muffins?

Freeze the zucchini muffins in small batches for breakfasts, snacks, or lunches.

Make a double back and freeze half of the muffins for later.

Place muffins in a freezer-safe bag or container, remove air and label. Store for up to 3 months in the freezer.

To thaw, place on the counter for several hours.

Make zucchini chocolate chip muffins

If you want, you can turn this recipe into one for gluten free chocolate chip zucchini muffins.

How? Just substitute the raisins with 1/2 cup chocolate chips!

Or you can do half chocolate chips and half raisins to make healthy chocolate zucchini muffins.

What kind of chocolate? I like to use semi-sweet chocolate like Enjoy Life Semi-Sweet Chocolate Mini-Chips, which is gluten free, dairy free and vegan.

If you’re not worried about allergies or food sensitivities, any type of chocolate chips – milk chocolate or semi-sweet – will do. And you can use regular or mini chocolate chips.

Make healthy zucchini muffins

Looking to make a healthy zucchini muffin recipe? Try these tips:

Sugar free substitutes: If you want, you can use Swerve Sweetener or powdered monk fruit sweetener instead of sugar.

Just use the equivalent (same) amount of Swerve or powdered monk fruit that you would sugar.

Can I use other sugars? Instead of white sugar, you can use the same amount of coconut sugar. Some people find that it’s a more wholesome substitute than refined sugar.

Go oil-free: You can make pumpkin zucchini muffins by substituting 1/2 cup pumpkin puree (not pumpkin pie mix) for the oil.

You can also substitute unsweetened apple sauce to make apple zucchini muffins.

If you use pureed bananas instead of the oil, then you’ll have banana zucchini muffins.

Vegan? If you’re vegan and want to make vegan zucchini muffins, use an egg replacer like Bob’s Red Mill Egg Replacer for the two eggs.

You could also use flax egg or aquafaba.

How much can I substitute? I would caution you about substituting both the oil and the eggs.

Maybe you could get away with all the oil and one egg and using more pumpkin/apple sauce/banana puree.

However, you may need to experiment with needing more/less flour, more/less baking powder or soda, or having to change baking temperature and times.

Can I add flax? Sure! Gluten-free baking tends to lack whole grains. So add a tablespoon of ground flax if you like. Your picky eaters won’t notice!

Can I make mini muffins?

Yes, you can make mini gluten-free zucchini muffins! You'll need a mini muffin pan and mini cupcake liners.

Adjust the baking time accordingly. I haven’t tried this yet, so I’m guessing you should check starting at 6 minutes, but the minis may be done around 8 or so.

Baking temperature and tips

I get a lot of feedback on my muffin recipes. People find the batter is too thick or too thin. Or they find the baking time is too short or too long.

Please, please, please do the following:

1. Read the recipe carefully.

2. Measure carefully. (Check out these easy tips on how to measure flour correctly.)

3. Read the section above on how to measure your flour. (You may be adding too much!)

4. Get an oven thermometer and make sure your oven temperature is accurate.

You’ll be shocked to find that your oven is too hot or not hot enough.

5. Set a timer and don’t walk away from the oven.

More healthy muffin recipes

Love gluten-free baking? These gluten-free muffins are perfect for beginners:

Try this Gluten-Free Applesauce Muffins Recipe made with easy-to-make homemade sugar-free apple sauce.

If you love yogurt or raspberries, you’re going to flip over this Raspberry Yogurt Muffins Recipe.

Got strawberries? Then make this Healthy Strawberry Muffins Recipe for breakfast.

These Banana Oatmeal Muffins make a terrific afternoon snack with a cup of tea or mug of coffee.

These Hash Brown Sausage Muffins are a savory make-ahead breakfast muffin.