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Healthy Zucchini Muffins

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

stacked zucchini muffins on wooden board with milk and cinnamon sticks in background

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. 

zucchini muffins on parchment paper on small board next to napkin

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.
avocado oil, whole grain flour, brown sugar, cinnamon, milk, egg, applesauce, vanilla extract, nutmeg, baking powder, soda and salt, and zucchini on white board

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.
hand using whisk in batter bowl with zucchini in top corner

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 in batter in mixing bowl next to image of batter in muffin pan

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.

zucchini muffins on wire rack, with milk and cinnamon sticks in top corner

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

Print

The Best Healthy Zucchini Muffins

stacked zucchini muffins on wooden board with milk and cinnamon sticks in background
Print Recipe

★★★★★

5 from 1 reviews

The best Healthy Zucchini Muffins! Spiced with cinnamon and nutmeg, made with whole grain flour and dairy-free. They can be made gluten-free friendly using a 1:1 gluten-free all-purpose baking flour. These muffins are perfect for garden season.

  • Author: Ashley
  • Prep Time: 10 minutes
  • Cook Time: 20 minutes
  • Total Time: 30 minutes
  • Yield: 12 muffins 1x
  • Category: breakfast
  • Method: oven
  • Cuisine: american

Ingredients

Scale

Dry Ingredients

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

  1. Preheat oven to 350ºF. Grease 12 cup muffin pan with oil; set aside.
  2. In a medium bowl whisk together flour, baking powder, baking soda, salt, ground cinnamon, and nutmeg; set aside.
  3. In a large bowl whisk together sugar and applesauce then whisk in oil, egg, milk and vanilla.
  4. 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.
  5. Evenly distribute batter into greased muffin pan, filling ¾ full (about heaping 1/4 cup of batter).
  6. 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.
  7. Transfer zucchini muffins to wire rack and allow to cool completely before storing. Muffins are best enjoyed fresh within 3 days.

Notes

Whole wheat white flour may be used, the muffins will just be slightly more dense. You can also use a mix of whole wheat and all-purpose flour. 1:1 all-purpose gluten-free baking flour should also work (make sure it is a 1:1 “baking” flour with xanthan gum).

I have not tested this with a vegan sub yet, but you should be able to use a flax seed egg.

Recipe adapted from my Whole Grain Cinnamon Apple Muffins.

Nutrition

  • Serving Size: 1/12
  • Calories: 146
  • Sugar: 12 g
  • Sodium: 132 mg
  • Fat: 5 g
  • Saturated Fat: 1 g
  • Unsaturated Fat: 4 g
  • Trans Fat: 0 g
  • Carbohydrates: 23 g
  • Fiber: 2 g
  • Protein: 3 g
  • Cholesterol: 16 mg

Keywords: zucchini muffins, healthy muffin recipes, whole wheat zucchini muffins

This post contains some affiliate links. Should you choose to purchase through said links, I will receive a small commission. Thank you for your support in helping keep Fit Mitten Kitchen up and running. 

Photography by About Dinner Thyme

About Ashley

"Ashley Walterhouse is the founder of Fit Mitten Kitchen, based in the Greater Lansing Area of Michigan, AKA “the Mitten.” Ashley grew up as a picky eater but later discovered that eating healthy was actually easy and fun. She started FMK in 2015 as a way to share her newfound love of developing healthier recipes for all to enjoy."

Reader Interactions

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  1. Shawna says

    Can’t wait to try this! I would like to know how many zucchini do you use in this recipe? It’s not posted in the list of ingredients! 🙂 Thanks!

    Reply

  3. Cassie Thuvan Tran says

    I LOVE zucchini muffins! They taste great alongside carrots and butternut squash in pastries–trust me on this one! Anyways, your batch looks absolutely heavenly. Even if it were really really hot or really really cold outside, I’d want all of the muffins you made!

    Reply

    • Ashley says

      Yep 🙂 You can use a non-dairy milk of your choice (I like cashew) or if not dairy-free cow’s milk is fine too. Eggs aren’t considered dairy, if that is what you’re wondering.

      Reply

  5. Sonya says

    I made these yesterday and they are delicious! I made two batches: one I made with chocolate chips. (For the kids), the other I subbed half the sugar for stevia and used 2 egg whites instead of one whole egg. It turned out really tasty. Great recipe!

    Reply

  6. Carolyn says

    Hi Ashley. Just want to verify an item. Do you measure the zucchini before or after you squeeze the water out?

    Love your focus in healthy recipes!

    Reply

  7. Ellen says

    Delicious muffins! Spicy and light. Will add some walnuts next time. I want to try the zucchini bread now.

    ★★★★★

    Reply

    • Ashley says

      Hello! I think honey could work, I wouldn’t Use less than 1/2 cup for flavor – the muffins as written aren’t super sweet. You could probably reduce the applesauce to 1/3 cup to compensate for the honey. Hope that helps!

      Reply