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 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, my neighbor makes Lil Luna’s 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.

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 27 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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Comments

  1. 4 stars
    Made these yesterday and was surprised that they didn’t have much of a lemon taste. Just how much lemon juice should you get from one lemon? Was thinking maybe I didn’t get enough juice from my lemon??
    I think I found why you say to use 2 percent or full fat yogurt. I only had non-fat and believe it could have been moister – but that was my fault for not following the directions.

    I did like the topping. I think it added a lot to the muffin.

  2. 4 stars
    Hi, my muffins came out very heavy not light and fluffy. I followed recipe to exactly. I did let the batter sit while I made the topping. What did I do wrong?
    I did not use aluminum free powder…

    1. Hi Jane. Hmm…do you usually bake with whole wheat flour? If not, this flour is more dense and heavy than white flour. In case, if you expect same lightness, these muffins will be a bit more dense. And of course not over mixing helps which sounds like you didn’t. Baking powder type doesn’t matter unless it’s not active anymore…

      1. 5 stars
        No I just started baking again after many years of not taking the time good to know! Thanks so much I have a lot to learn!

        1. Happy to have you here learning, feel free to ask any questions at any time! 🙂

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