It’s time to use up all of those delicious summer squash growing in your garden by whipping up a batch of these Healthy Zucchini Muffins!  Not only are these zucchini muffins bursting with fresh lemon flavor, but they are also gluten-free, grain-free, Paleo, refined sugar-free, and can easily be made vegan!

A pile of easy healthy zucchini muffins on a table with a lemon slice.

Summer = Gardens + Zucchini Muffins!!

For the past few years, Cohl has grown a beautiful summer garden for us.  He totally has the green thumb while mine is more of a brown thumb!

Since we live in Texas and our summers can get pretty toasty (and very dry!) he decided to forgo the summer garden and wait it out until winter.  I don’t blame him a bit, but man do I miss all of the fresh summer produce!

In addition to an abundance of cherry tomatoes, summer squash always seemed to flourish in our summer gardens.  Oftentimes we had zucchini growing out of our ears and were scrounging about looking for new recipes to try.

Last week I posted this Sauteed Zucchini & Squash recipe which is one of our go-tos for using up summer squash, as well as this Healthy Summer Squash Casserole.  However, if you’re tired of the savory recipes, you’ve got to stay tuned for these Healthy Zucchini Muffins!  (YES… healthy!)

A picture of easy zucchini muffins with a whole zucchini on the side.

How are these Healthy Zucchini Muffins?

I do not say “healthy” zucchini muffins here loosely.  These totally are good-for-you muffins that you can actually eat for breakfast!

So what exactly makes these zucchini muffins healthy?  They are:

  • Grain-free.  Almond flour and tapioca starch replace the wheat flour.
  • Gluten-free.
  • Refined-sugar free.  Maple syrup and coconut sugar replace the refined white sugar.
  • Dairy-free.  Coconut oil is used in place of butter.
  • Loaded with nutrition.  Almond flour adds extra Vitamin E and Magnesium while the zucchini bumps up the Vitamin A and Vitamin C.
  • And they can easily be made vegan!!

Shredded zucchini inside a food processor to make a zucchini muffin recipe.

How Do You Make Shredded Zucchini?

One of the key steps in making these healthy zucchini muffins is shredding the zucchini and then dabbing the excess liquid that is released.

So how do you make shredded zucchini?

The easiest way I have found to do this, and the least dangerous to your fingers!, is to use a food processor with the shredding attachment.

If you’re brave and don’t happen to have a food processor you can always use a cheese grater.  But please, be careful!

Gluten-free zucchini muffin with a bite inside surrounded by other muffins.

How Can You Evolve these Healthy Zucchini Muffins?

While these lemon zucchini muffins are already gluten-free, grain-free, Paleo, vegetarian, dairy-free, and refined sugar free, there are a few ways you can change them up:

  • Want to make them vegan?  Simply use 2 flax eggs in place of the regular eggs.
  • Not a fan of lemon?  Lime juice and zest will work great in these healthy zucchini muffins, too.
  • Don’t have any almond butter?  Feel free to use peanut or cashew butter in place of the almond butter.  (Just note, they won’t be Paleo if peanut butter is used!)
  • Want to make a gluten-free Zucchini Bread recipe, instead?  All you need is an all purpose gluten-free flour and a loaf pan!

One lemon zucchini muffin with a bite inside on top of another muffin for breakfast.

Want more Healthy Muffin Recipes?

Gluten Free + Paleo Carrot Cake Muffins

Paleo Chocolate Banana Muffins

Healthy Pumpkin Muffins

Cinnamon Muffins

Zucchini Chocolate Chip Muffins

Tap stars to rate!

4.08 from 13 votes

Healthy Lemon Zucchini Muffins | Paleo, Gluten Free

It's time to use up all of those delicious summer squash growing in your garden by whipping up a batch of these Healthy Zucchini Muffins!  Not only are these zucchini muffins bursting with fresh lemon flavor, but they are also gluten-free, grain-free, Paleo, refined sugar-free, and can easily be made vegan!
Yield 12 muffins
Prep 10 minutes
Cook 25 minutes
Total 35 minutes
An image of an envelope sealed shut with the Evolving Table logo.

Email this recipe!

Enter your email and we'll send it directly to you.


  • 2 cups zucchini finely grated
  • 2 eggs
  • 1 tsp vanilla
  • ¼ cup coconut sugar
  • ¼ cup pure maple syrup
  • ¼ cup almond butter smooth
  • 1/3 cup coconut oil melted
  • ½ cup tapioca starch
  • 1 ½ cup almond flour bleached
  • 1 tsp. baking soda
  • ½ tsp. salt
  • 2 Tbsp. lemon juice
  • 2 Tbsp. lemon zest
  • ¼ cup sliced almonds optional


  • Preheat oven to 350 degrees.
  • Using a food processor, finely grate the zucchini. Measure out 2 cups. Squeeze all of the excess water out of the zucchini. (You will end up with a little over 1 cup of grated zucchini once water is squeezed out.)
  • In a large bowl combine eggs, vanilla, sugar, syrup, almond butter, and oil. Whisk until combined.
  • In a separate medium-sized bowl combine starch, almond flour, baking soda and salt. Whisk to combine.
  • Add dry ingredients to wet ingredients and stir until just combined. Next, add shredded zucchini, lemon juice and lemon zest. Mix until just combined, being careful not to over mix.
  • Line a regular-sized muffin tray with cupcake liners. Spray liners with non-stick cooking spray and fill to 3/4 full. Top each with 1 teaspoon sliced almonds.
  • Bake for 23-25 minutes, or until a toothpick when inserted in comes out clean.
  • Let cool for 10 minutes before serving and enjoy!
Last step! If you make this, please leave a review letting us know how it was!

Tap stars to rate!

4.08 from 13 votes


Calories: 225kcal, Carbohydrates: 17g, Protein: 5g, Fat: 16g, Saturated Fat: 6g, Cholesterol: 27mg, Sodium: 211mg, Potassium: 122mg, Fiber: 2g, Sugar: 7g, Vitamin A: 80IU, Vitamin C: 7.8mg, Calcium: 65mg, Iron: 1mg

Nutrition information is automatically calculated, so should only be used as an approximation.

Made this recipe?Leave a comment below!
5 Secrets to Healthier Family Dinners
Tips & recipes for getting yummy — and healthy — meals on the table.

You May Also Like

Thanks for
Stopping By!

I’m London! Join me as we cook up nourishing meals for you and your loved ones and learn a few healthy cooking tips and tricks!

Leave a comment

Your email address will not be published. Required fields are marked *

Recipe Rating


  1. Hello London,
    This recipe looks divine, and I will be trying it
    very soon.

    Would you be able to advise bake time for this recipe as mini muffins, please? I would like to bake these for a party.

    1. Mini muffins will cook up in about 2/3 to 3/4 the time. So I’d start taking a look at the muffins around 15 minutes. They’ll probably be done by 17 minutes or so! Can’t wait to hear what you think about the recipe 🙂

  2. 5 stars
    Beautiful, moist, delicious cake! I did not add the nuts to the mix or the top. Otherwise, no changes made to the recipe. I can’t wait to take them to a ladies retreat tomorrow and share with my friends. I am saving this one!

    1. Yay, Michelle! So happy you enjoyed the recipe so much. Hope your ladies enjoy them, too. Thanks for your comment and rating! 🙂

  3. 5 stars
    Made these tonight and they are delicious! Thank you for sharing this recipe. Do you store leftovers in the refrigerator or in a covered container at room temp?

    1. So happy you enjoyed them, Cheryl! If you want them to last a little longer, you can store them in the refrigerator. If left out on the counter, you have about 2-3 days in an airtight container!

  4. I was so closely following the recipe that I almost did not add the zucchini. I saw it sitting on the counter, reread the recipe and realized it doesn’t tell you when to add the zucchini. It doesn’t take a genius to know to add it near the end, perhaps with the lemon juice and zest. I did that. The batter tastes great. The muffins are in the oven right now. Looking forward to trying the finished product. Just a comment to let you know of the minor flaw in the written recipe. Thanks.

    1. Hi!! Thank you SO much for pointing this out. And yes, it gets added in with the lemon juice and zest! I have updated the recipe to reflect this. Thanks again for your help!

  5. 5 stars
    I made these tonight and they are delicious. I did make a couple of substitutions, date sugar in place of coconut sugar, 1/2 the amount of the maple sugar, and cashew butter instead of almond butter. They turned out really good.

    1. So happy to hear you enjoyed them, Michele! And I love your substitution ideas!! Will have to try those out next time 🙂 Thanks for the comment and rating!

  6. These muffins look awesome! Loving all the healthy swaps here. Definitely gonna try these. Thanks for the great recipe????

    1. Thanks so much, Ashley!! These are definitely not your normal muffin 😉 Can’t wait to hear what you think when you try them!

    2. Hi, I’m making these now, I have 12 muffin liners filled and I still have a lot left over? Did I do something wrong? And is it supposed to be in the thinner side? Thanks

      1. Hi Ashley!! Apologies for just now responding, but hoping the muffins turned out OK! The batter is slightly thin, but could be a bit too watery if the zucchini was not thoroughly dried. Also, different muffin trays can vary slightly in size so this might be the cause of having too much batter. Would love to know how it turned out for you!