Light and fluffy healthy Zucchini Muffins! Spiced with cinnamon and nutmeg, made with whole grain flour and dairy free. You will love these!

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Zucchini muffins and zucchini bread always bring me back to my childhood. My mom used to bake a delicious zucchini bread, with extra cinnamon, and I can picture foil wrapped loafs in the freezer.
I also remember thinking “Why do I like zucchini bread but not zucchini plain?”
SUGAR, of course.
This zucchini muffin recipe is reminiscent of the traditional classic zucchini bread recipe, but made with whole grain flour, lightened up with applesauce, and still moist thanks to some oil and zucchini.
Why You Should Make These
- This recipe uses basic healthy pantry staples.
- They’re a great recipe to use up some fresh garden zucchini.
- Zucchini muffins make the best snack, loved by both kids and adults.
- You can add chocolate chips!
The “hardest” part is grating the zucchini – which tends to find its way to the floor when grating. Thankfully Gilly didn’t mind the zucchini shreds on the floor and picked them up for me. Dog vacuums are the best.

What’s in Healthy Zucchini Muffins
- zucchini – use freshly grated zucchini, water squeezed out.
- applesauce & oil – the combination of applesauce with oil creates the perfect balance of softness and moisture.
- brown sugar – the sweetener of choice for this zucchini muffin recipe. You can also use another granulated sweetemer of choice (I don’t recommend subbing honey or maple syrup here)
- egg – helps hold everything together. A flaxseed egg may work here as well, but that has not been tested.
- vanilla extract – adds lovely flavor.
- milk of choice (I used cashew) – to help thin out the batter slightly.
- whole grain flour or 1:1 gluten-free all-purpose baking flour – Use a whole wheat pastry flour or 1:1 gluten-free all-purpose baking flour. OR whole wheat and all-purpose on hand, do half of each.
- baking powder, baking soda and salt – to help get the right rise in the muffins, and salt balances flavor.
- cinnamon & nutmeg – lots of cinnamon and a touch of nutmeg in these easy zucchini muffins! If you’re not a fan of nutmeg, simply omit.

Recommended Baking Tools
- Box Grater, use the fine side for this recipe.
- Fine mesh bags, if you bake with zucchini a lot, these are great.
- 12-Cup Muffin Pan, use a light colored muffin pan or silicone cups are great too.
- Medium Cookie Scoop, for dispensing batter.

Some Notes
- Shredded Zucchini – I like to use the fine side of the box grater for this recipe, and make sure to squeeze out all of the water before adding to the mixing bowl.
- Batter Tip – I like to use my medium cookie scoop for dispensing the batter into the muffin pan – makes less of a mess and it’s quicker!
- The sugar – I would use 2/3 cup of sugar as noted in the recipe page but you can get away with a half cup if your sweet tooth isn’t strong. OR you could even add about 1/3 cup mini chocolate chips. I opted for a granulated sweetener here.

Zucchini Muffin Mix-ins
Chocolate Chips – Make this recipe into Zucchini Chocolate Chip Muffins by adding 1/2 cup mini chocolate chips.
Blueberries – I love a good blueberry muffin recipe. You can add blueberries to this one, or I have this recipe as well.
Chopped Walnuts – If you like a little crunch in your muffins, add some chopped toasted walnuts.
Craisins – Adding dried cranberries would give these a little extra sweetness. If you love lots of texture in your muffins, adding craising and walnuts together would be delicious.

I hope you put these healthy zucchini muffins on your list! They’re soft and fluffy and taste amazing with almond butter!
More Ways to Bake with Zucchini
Let me know if you make this recipe by leaving a comment and rating below! It helps others learn more about the recipe too. Xx Ashley
The Best Healthy Zucchini Muffins
Ingredients
Dry Ingredients
- 1 3/4 cup + 2 TBSP whole wheat pastry flour1
- 1/2 tsp baking soda
- 1/2 tsp baking powder
- 1/4 tsp salt
- 2 tsp cinnamon
- 1/4 tsp ground nutmeg
Wet Ingredients
- 2/3 cup coconut sugar or brown sugar2
- 1/2 cup applesauce3
- 1/3 cup oil, avocado, sunflower, melted & cooled coconut
- 1 large egg
- 1/4 cup milk of choice, I used cashew
- 1 tsp vanilla extract
- 1 1/2 cups lightly packed shredded zucchini, water squeezed out (equal to about 1 medium zucchini)
Instructions
- Preheat oven to 350ºF. Grease 12 cup muffin pan with oil; set aside.
- In a medium bowl whisk together flour, baking powder, baking soda, salt, ground cinnamon, and nutmeg; set aside.
- In a large bowl whisk together sugar and applesauce then whisk in oil, egg, milk and vanilla.
- Add bowl of dry ingredients into large bowl of wet ingredients. Using large spatula, gently combine until dry ingredients are almost incorporated, then fold in shredded zucchini. Batter will be somewhat thick. Avoid over-mixing the batter or you’ll end up with tough muffins.
- Evenly distribute batter into greased muffin pan, filling ¾ full (about heaping 1/4 cup of batter).
- Bake muffins at 350ºF for 15-20 minutes, or until inserted toothpick in center of muffin comes out clean. Allow muffins to cool in pan for about 10-15 minutes before gently removing. TIP: if greasing pan, I use a butter knife to remove from pan.
- Transfer zucchini muffins to wire rack and allow to cool completely before storing. Muffins are best enjoyed fresh within 3 days.
Recipe Notes:
Nutrition Information
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Photography by About Dinner Thyme













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