Healthy Lemon Zucchini Muffins are incredibly moist, fluffy and bursting with fresh lemon flavor. They are perfect to take advantage of garden fresh zucchini bounty and make a great choice for healthy breakfast or snack!

I love baking with zucchini during summer. Other favorites include healthy banana zucchini muffins, zucchini carrot muffins and healthy zucchini muffins!

Healthy lemon zucchini muffins on a cooling rack with fresh lemon.

These healthy lemon zucchini muffins are light, lemony and so moist! Contain only simple ingredients and are so easy to make.

Made with whole wheat flour, plain yogurt, zucchini and a coconut flake topping. Although the topping is optional, it is extremely delicious and adds another layer of fresh lemon flavor!

Every summer, I make my lemon zucchini bread which in turn inspired these healthy zucchini lemon muffins.

I now have a version of my own healthy lemon zucchini bread too. It is 100% healthy, naturally gluten free, and will blow your mind how amazing it tastes!

Of course, my end results ended up being completely different, just like most of my healthy muffin recipes. Lighter and better for you being the name of the game!

What Makes These Muffins Healthy?

  • More veggies: No one will notice they are getting an extra serving of zucchini!
  • Low oil: Both zucchini and yogurt add moisture while keeping added oil to a minimum.
  • Flavorful: Lemon adds a zing of flavor you are going to love!
  • Wholesome: Whole wheat flour or spelt flour adds nutritious fiber that keeps you full longer and natural sweetener means you avoid a sugar crash later. You’re welcome!
  • Optional topping: Makes muffins taste indulgent and doubles for a healthy dessert.

Ingredients You’ll Need

Yogurt, lemon, zucchini, oats, eggs, oil, maple syrup, whole wheat flour, coconut flakes, vanilla extract, baking powder, baking soda, salt.
  • Zucchini: Shred zucchini using medium size holes to help incorporate better with the batter. Give a gentle squeeze.
  • Yogurt: Use plain yogurt or Greek yogurt with fat content 2% and higher. Non-fat yogurt lacks flavor and moisture.
  • Lemon: You want to use only fresh lemon juice and zest. Bottled doesn’t taste nearly the same. Not to mention it is loaded with preservatives.
  • Whole wheat or spelt flour: Please stick to these 2 flours for most favorable end result. Baking is a science, all flours are different and do not act the same.
  • Oil: We use just 2 tbsp, and any mild tasting oil will work. I often use avocado oil.
  • Maple syrup: Any liquid sweetener like honey, agave or brown rice syrup will work. Do not use sugar as it is dry and batter consistency will be thrown off.
  • Eggs: For lift and binding, you can replace eggs with flax eggs.
  • Muffin topping (optional): Rolled or quick oats, honey or maple syrup, coconut or avocado oil, lemon zest, unsweetened coconut flakes.

How to Make Healthy Lemon Zucchini Muffins

These healthy zucchini lemon muffins come together in one bowl, two if you are making the optional topping!

Muffin batter in red muffin tin.
  1. Prep: Preheat oven to 350 degrees F and line muffin tin with paper liners. Alternately, use a silicone muffin pan. Shred zucchini and give it a gentle squeeze. Juice and zest lemon.
  2. Make muffin batter: In a large mixing bowl, add eggs, yogurt, maple syrup, oil, lemon juice, lemon zest, shredded zucchini, baking powder, baking soda, and salt; whisk well to combine. Add flour and stir gently to mix. Do not over mix which could lead to dense muffins.
  3. Make topping (optional): In a different smaller bowl, add all topping ingredients and stir to combine.
  4. Fill muffin pan and bake: Using large ice cream scoop, fill 12 openings with batter and if using the topping sprinkle that on top. Bake for 25 minutes or until toothpick inserted in the middle comes out clean.
  5. Cool: Remove from the oven and let muffins cool in the tin for 10 minutes before transferring onto a cooling rack to cool off more.

Suggested Variations

Tips for Best Results

  • Whisk well, but stir soft: This tip applies to this muffin and others! Whisk your wet ingredients well or briskly to ensure all your baking staples are dissolved but once you add your flour or other add-ins fold gently. This ensures light and airy baked goods!
  • Use a trigger release scoop. When dividing the batter, this is super helpful in getting equal portions. This helps to ensure each muffin gets evenly baked.
  • No need to peel your zucchini: Zucchini skin is very thin, so there is no need to peel, plus the green flecks look so colorful.
  • Zesting the lemon: Microplane is the best for zesting lemon. In a pinch, box grater will work. Just make sure to zest only yellow part as white pith can add bitter taste to the muffins.

FAQs

Could I use summer squash vs. zucchini?

I have not tested it with yellow squash, but they usually can be used interchangeably. Be sure to let me know how it goes in the comments!

What could I substitute for yogurt?

You could try applesauce or mashed banana.

Can I use a different flour?

Baking is a science and using different flours other than the tested whole wheat flour or spelt flour could lead to undesirable muffin results! That being said, you could try 1:1 whole wheat white flour or whole wheat pastry flour substitute.

All purpose flour could be tried, but you will need less or your muffins will be dry.

Can I make mini muffins?

Yes. You just want to keep an eye on them and lower the baking time. Bake them for 12-15 minutes and check.

Storing and Freezing Tips

I bake muffins all the time because kids love them! I always double or even triple any muffin recipe for freezing.

To store: If not freezing, I store baked muffins on a plate on a kitchen counter covered with a towel for first 2 days. If any are left at that point (let’s be honest), I transfer them to a container with a lid and into the fridge for another 3 days.

I mean this is fantasy I am talking about here. I have 3 men in the house who eat 24 muffins within 24 hours.

To freeze muffins: Bake, cool and place in a gallon size Ziploc container. Release as much air as possible and seal. Freeze for up to 3 months. To thaw, just place on a counter for a few hours.

Storage Tip

Be sure to check out my best practices posts how to store muffins and how to freeze muffins to keep your leftover muffins fresh longer.

More Healthy Lemon and Zucchini Recipes

Healthy lemon zucchini muffins on baking rack with one muffin split open.
Healthy lemon zucchini muffins on cooling rack with fresh lemon and zucchini.

Healthy Lemon Zucchini Muffins

Healthy Lemon Zucchini Muffins are incredibly moist, fluffy and bursting with fresh lemon flavor. Perfect to use up garden fresh zucchini!
4.86 from 28 votes
Servings 12 muffins
Calories 189
Diet Low Fat
Prep Time 10 minutes
Cook Time 25 minutes
Cooling Time 20 minutes
Total Time 55 minutes

Ingredients  

  • 2 large eggs
  • 1/2 cup plain yogurt or Greek yogurt 2% + fat
  • 1/2 cup maple syrup or honey
  • 2 tbsp any mild tasting oil
  • 1 large lemon zest and juice of
  • 2 cups shredded zucchini on medium hole lightly squeezed
  • 2 tsp baking powder
  • 1/2 tsp baking soda
  • 1/4 tsp salt
  • 2 1/3 cups whole wheat flour or spelt flour

Topping (optional):

Instructions 

  • Preheat oven to 350 degrees F and line muffin tin with liners or use silicone muffin tin.
  • In a large mixing bowl, add eggs, yogurt, maple syrup, oil, lemon juice, lemon zest, zucchini, baking powder, baking soda, and salt; whisk well to combine. Add flour and stir gently to mix. Do not over mix.
  • To make optional topping: In a small bowl, add oats, honey, oil, lemon zest, coconut flakes and mix with a spoon.
  • Using large ice cream scoop, fill 12 openings with batter and spoon topping on top (if using). Bake for 25 minutes or until toothpick inserted in the middle comes out clean.
  • Remove from the oven and let muffins cool in the tin for 10 minutes before transferring onto a cooling rack to cool off more.

Notes

  • Store: On a plate on a kitchen counter covered with a towel for first 2 days. Then transfer them to a container with a lid and into the fridge for another 3 days.
  • Freeze: Bake, cool and place in a gallon size Ziploc container. Release as much air as possible and seal. Freeze for up to 3 months. To thaw, just place on a counter for a few hours.
  • Lemon: Only fresh. Bottled doesn’t taste nearly the same. Not to mention it is loaded with preservatives.
  • Whole wheat or spelt flour: Please stick to these 2 flours for most favorable end result. Baking is a science. All flours are so different. They do not act the same.
  • Maple syrup: Any liquid sweetener like honey, agave or brown rice syrup will work. Do not use sugar as it is dry and batter consistency will be thrown off.
  • Eggs: You can replace eggs with flax eggs.

Nutrition

Serving: 1muffin | Calories: 189kcal | Carbohydrates: 31g | Protein: 5g | Fat: 6g | Saturated Fat: 2g | Cholesterol: 29mg | Sodium: 202mg | Fiber: 3g | Sugar: 11g
Course: Muffins
Cuisine: North American
Author: Olena Osipov
Did you make this recipe?Mention @ifoodreal or tag #ifoodreal!

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About Olena

Welcome! I grew up in Ukraine watching my grandma cook with simple ingredients. I have spent the last 14 years making it my mission to help you cook quick and easy meals for your family!

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Comments

  1. 5 stars
    I made these today and they are delicious! I only had 0 fat yogurt so I added a little bit more oil. I didnโ€™t make the topping but I added blueberries. OMG it was perfect with the lemon. So moist and tasty! Iโ€™ll be making these again!

  2. 4 stars
    Hello Olena.

    I have made these muffins quite a few times now. The flavors are so delicious together I can:t get enough! However, everytime I make them, they always sink in the middle. They rise beautifully but sink within seconds after I take them out. My baking powder and soda are fine, and I did not make any changes to the recipe, except for adding more lemon zest.. Any idea what might have happened? Too much moisture from the zucchini, maybe?
    Thanks for sharing all your delicious and healthy recipes.

    1. Hmm. If you use garden zucchini joe squash they do contain more moisture. Or could be the altitude so you can Google how to adjust baking for it. Also if you add a few more tbsp of flour so bather is thicker it would help with higher muffin tops. Good luck!

  3. 5 stars
    Very tasty!! I only had 1 1/2 cups of zucchini so I substituted shredded carrot for the last 1/4 cup and they turned out fine. For the large lemon contents I used 3 tbs of juice and 1 tbs of zest but I think I will add a little more zest in next time. Multigrain flour worked well as I didn’t have whole wheat or spelt flour. The topping is to die for….love it. I will definitely be making these again and sharing the recipe!!! Thank you!

  4. 5 stars
    These are very good and my husband even likes them. I left off the topping. I had enough batter and ended up with 16 muffins.

  5. 5 stars
    Hello Olena.

    These look awesome! I have two questions, though.

    First, in the instructions you say once baked you need to let the muffins cool in the muffin tin for 60 minutes before transfering them to a cooling rack. Is this the case? Will they not become soggy if left to cool off inside the tin for 1 whole hour?
    Second, do you think this recipe can be made into a loaf? If possible, will ingredients need adjusting?and what would be the new baking time?
    Im fairly new to baking so Im still trying to understand the logic behind things.
    Awaiting for your reply. Thanks! Can’t wait to try these!

    1. You can take muffins out of the muffin tin after 20-30 mins. Doesn’t matter. No, they won’t become soggy. I never baked this bread as a loaf but probably it will work. As a new baker I would recommend to follow recipes first until you get comfortable. Sometimes breads workout from a muffin batter and sometimes don’t.

  6. 5 stars
    Hello Olena
    What would be the cooking time if i made 24 mini muffins instead of 12 regular ones? My kids like mini muffins.
    Thanks.

  7. 4 stars
    Moist tasty and lemony, great recipe. I substituted a combination of brown rice flour and buckwheat flour and it worked well.

  8. 5 stars
    I’ve been making these muffins for a year and each time I don’t have all of some ingredient. This time, I substituted lime zest and juice for some of the lemon additives and it was great! I do add fresh blueberries and enjoy the added moisture it provides. I wish I could ship a bunch of zucchini to anyone who needs it to make this recipe. They are coming in like crazy from the garden!

    1. So happy to hear. We have had weeks of heat wave but it will start raining shortly so I will bake these too. I have so many bananas to use up though will do my banana zucchini muffins. And I know what you mean about zucchini. I have so many gigs coming up, no one to share with. I would take your zucchini in a heartbeat.

4.86 from 28 votes (2 ratings without comment)

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