Gluten-free zucchini muffins are easy to make, naturally sweetened, and absolutely delicious. Not sure about zucchini in muffins? If the idea surprises your family, just don’t mention it. Once they’ve polished off one of these soft, moist muffins, then you can let them in on the secret. With applesauce and honey instead of white sugar, these muffins feel wholesome but taste like a bakery treat. Perfect for breakfast, snacks, or packing in lunchboxes—bake a batch and see for yourself.
I may have gotten a little carried away at the farmers market—too much zucchini, and then I realized I'd be home alone for the week. Oops. I love grilling zucchini, sautéing it, or spiralizing it into zucchini noodles, but I wanted to try something different. Baking sounded like just the thing—and it turns out, these muffins were the perfect solution for too much zucchini.
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Why You'll Love This Recipe
- Soft, moist, and naturally sweet – Just applesauce and honey.
- Easy to make and freezer-friendly – Great for meal prep, snacks, or quick breakfasts.
- A smart way to use extra zucchini – Win over even the skeptical eaters.
Recipe Ingredients
- Gluten-free flour blend – I use King Arthur Measure for Measure; it performs well without needing additional binders.
- Aluminum-free baking powder – Gives lift with a clean flavor.
- Baking soda – Reacts with the applesauce and honey for added rise and browning.
- Cinnamon – Adds warmth and subtle complexity.
- Unsweetened applesauce – Naturally sweetens the muffins and keeps them moist
- Mild honey – Adds gentle sweetness and pairs well with the zucchini and spice.
- Egg – Binds the batter and helps with structure.
- Vanilla extract – Enhances the overall flavor.
- Oil – Coconut oil (melted), avocado oil, or a healthy neutral oil, keeps the muffins tender and dairy-free.
- Zucchini – Grate and squeeze dry to remove excess moisture.
Substitutions and Variations
- Add orange zest – Brightens the flavor with a hint of citrus.
- Try Five Spice instead of cinnamon.
- Chopped walnuts – Add crunch and richness if desired.
Please see recipe card for measurements and salt.
Recipe Instructions
Zucchini, like all vegetables, contain a lot of water. To bake with zucchini, grate it on the large holes of a box grater, then place grated zucchini in layers of paper towels or a clean kitchen towel and squeeze it dry.
Chef's tool tip on digital kitchen scales: When baking, weigh them using a digital kitchen scale. Weighing dry ingredients (especially gluten-free flours) gives you the best results, is fast and accurate. A scale is an inexpensive and terrific investment if you don’t have one.
Baking Tips for Success
- Use light colored metal muffin pans to bake, not the dark ones. It makes a difference.
- Skip paper liners and spray wells with non-stick or oil with coconut oil
- Remove the baked muffins from the pan right after baking. They will be soft, so handle gently. You don’t want them to steam in the pan. Cool on a wire rack.
- To easily remove muffins from pan, use a mini off-set spatula. It is a handy and inexpensive too for many things in the kitchen.
Serving Suggestions
- Serve zucchini muffins warm with coffee or tea for a light breakfast
- As a snack with a smear of almond, peanut butte, or maple butter.
- Packed in lunchboxes for kids or grown-ups
- Alongside eggs, yogurt, and a fresh fruit salad for a balanced morning meal.
- With a drizzle of honey or maple syrup if you want a touch more sweetness.
Storing and Freezing
Let muffins cool completely, then store them in an airtight container or zip-top bag at room temperature for up to 4–5 days. For best freshness, keep them in a cool, dry spot out of direct sunlight.
Gluten-free zucchini muffins freeze very well. Let them cool completely, then wrap tightly or store in a freezer-safe container. Thaw at room temp or rewarm gently.
Recipe FAQs
There’s no need to peel zucchini before making muffins. The skin is thin and softens during baking. Plus, it adds color and nutrients.
Not really. It adds moisture and softness, but the flavor is mild and blends in with the applesauce, honey, and spice.
Yes. Use a flax egg, chia egg, or egg replacer. The texture may be slightly softer, but should work well.
More Baking Recipes
There's nothing like a homemade baked treat that's healthy and easy to make too. Try one of these easy baking recipes. They are all gluten-free.
Did You Make This Recipe?
If you make these gluten-free zucchini muffins, please add your comment. I appreciate your feedback and enjoy hearing from you. If you loved it, please give it a 5-star rating! They really help other readers.
📖 Recipe
Zucchini Applesauce Muffins
Equipment
- Light colored 12-cup muffin pan
Ingredients
Muffins
- 2 cups GF flour blend I use King Arthur measure for Measure
- 1 ½ teaspoons aluminum-free baking powder
- 1 teaspoon baking soda
- ¾ teaspoon Cinnamon or Chinese five Spice
- ¼ teaspoon salt
- 1 ½ cups unsweetened applesauce 13 ounces
- ½ cup mild honey
- 1 large egg
- 1 large orange zested
- 1 teaspoon vanilla extract
- ⅓ cup coconut oil melted if solid
- 8 ounces zucchini 1 ⅓ cups after grating a squeezing dry
- ¾ cup chopped walnuts optional
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Instructions
- Pre-heat oven to 325ºF. Blend flours: Weigh flours in a bowl on a digital kitchen scale. Whisk together well to combine completely. Place in an airtight container and label. You will use part for the muffins and have extra for another baking project.
- Add 285 grams (2 cups) of the flour blend to the bowl, then add in salt, spice, baking powder and soda. Whisk well to combine.
- In a separate bowl, stir applesauce honey, egg, zest, vanilla, and oil. Add dry ingredients to wet ingredients. Using a hand electric mixer, beat on medium high for 1-2 minutes.
- For zucchini, trim off ends and grate on the large holes of a box grater. Place grated zucchini on layers of paper towels or a clean kitchen towel and squeeze out as much moisture as possible. You want dry zucchini. Next, fold zucchini and walnuts into batter.
- Spray a light colored standard size muffin pan with non-stick spray. Portion batter evenly into the wells. Bake for approximately 32 minutes or until muffins are golden brown and firm to the touch, and a toothpick inserted into the center comes out clean.
- Remove pan from oven and carefully remove each muffin to a wire rack to cook as quickly as possible. Don’t let them sit in the pan and steam. Enjoy warm or cool completely and store at room temperature in a zip bag. Muffins will keep for a few days.
Notes
Nutrition
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Olga says
Can't wait to try these!! Could I use plain flour, or spelt flour, instead of the mix? I like things simple and can tolerate flour, wheat and gluten quite well.
Sally Cameron says
Hi Olga, as I bake gluten-free I've never tried it with wheat flour. It might work but not sure. The simple way to make them is to use Bob’s Red Mill all-purpose gluten-free flour blend. The one I've been using lately is in the blue bag, called 1:1. It's widely available. You don't have to blend your own flour if that a hassle. Hope that helps!
Ordinary Blogger says
I have SO MUCH zucchini right now and this looks like a lovely alternative to zucchini bread. Thanks for the inspiration!
Sally says
Try the grilled zucchini and the zucchini gratin. I love zucchini too!
Marion Tinney says
Instead of grams, how many cups of flour are needed?
Sally says
Marion, I did not list cups because gluten-free flours really need to be weighed, or you might not get the same results. Do you have a scale? They are such fantastic tool, and inexpensive too. I have to make them again Sunday for a client. I will figure it out and make a note, ok?
Sally says
HI Marion. I've updated the recipe with cups! Made a batch this morning. Hope this helps. Happy baking, Sally.
Madonna/aka/Ms. Lemon says
These look delicious Sally. Love the use of 5 spice.
Madonna
Sally says
Five spice is so fun and just a little different. Great affinity for chocolate too! Ever tried that?