Skip to main content

Paleo Zucchini Chocolate Chip Muffins ( Gluten Free, Dairy Free)

By September 12, 2022June 4th, 2024Breads and Muffins, Dairy Free, Gluten Free, Paleo

These muffins are beautifully moist, deliciously sweet and incredibly healthy. They’re high in protein, perfect for your morning breakfast or afternoon snack. Zucchini and chocolate chips are mixed into a grain and dairy free muffin batter and topped with the perfect crumble. Kids love them.

Paleo Zucchini Chocolate Chip Muffins a pile of muffins

I created these muffins as a healthy snack for my grandson Avery. I’m always trying to encourage him to eat more vegetables. They contain lots of zucchini but it’s hidden, you can’t taste it and hardly see it.

There’s just a little bit of chocolate chips to make the muffins fun and sweet. They have a little crunch from the crumb topping. It’s such a satisfying texture.

Paleo Zucchini Chocolate Chip Muffins Avery eating a muffin

These muffins are every bit as delicious as a standard muffin just more nutritious. This recipe utilizes whole ingredients that are full of vitamins and nutrients including a bit of almond butter for extra protein to help stabilize your blood sugar and keep you satisfied for hours.

Paleo Zucchini Chocolate Chip Muffins pan with chips

Ingredients For Zucchini Chocolate Chip Muffins

Ingredient List

In this recipe I use basic baking ingredients like baking soda, vanilla extract and salt but everything else is nutrient rich making these muffins super healthy. Here’s the list:

  • Almond Flour – Use blanched almond flour for a light texture! It’s a high protein flour that provides structure for your muffins and fiber to keep you full!
  • Pastured Eggs – They hold the muffins together, make them fluffy and boost the protein. The best type of eggs come from pastured free-range chickens, where the birds are allowed to roam.  The chickens are happy and they contain 2-3 times as many nutrients.
  • Creamy Almond ButterAlmond butter makes these muffins richer tasting and gives them a creamy texture. It provides additional protein and healthy fats.  Cashew butter or peanut butter can be used as well.
  • Coconut Oil – Is used as a healthy fat to make the muffins moist. It contains medium-chain fatty acids and has anti-inflammatory, anti-microbial and anti-fungal properties.
  • Coconut Sugar or Maple Sugar– Creates a sweet taste and is more nutritious and lower on the glycemic index than refined sugar.
  • Dairy Free Mini Dark Chocolate Chips– These contain the chocolate flavor with none of the dairy! Dark chocolate is loaded with antioxidants and magnesium to calm stress.
  • Lemon Juice – A chemical reaction occurs when lemon juice mixes with baking soda helping the muffins rise properly.
  • Tapioca Flour – Naturally gluten free, it gives the muffins a fluffy and spongy texture.

Paleo Zucchini Chocolate Chip Muffins ingredients

Zucchini –  Here we shred the zucchini and then squeeze out the water in a kitchen towel. This is an important step. If there is too much water in the zucchini the muffins won’t rise properly. Really squeeze out the water to get a light fluffy muffin.

Paleo Zucchini Chocolate Chip Muffins zucchini in towelPaleo Zucchini Chocolate Chip Muffins zucchini mixed into batter

Muffin Making Tips

  • Don’t Overmix – Overmixing can cause the muffins to be tough and bake unevenly. Gently fold in the zucchini and chips.
  • Get It Into The Pan Quickly – The lemon and baking soda form a chemical reaction. Getting them into the oven quickly helps make the muffins nice and fluffy. Immediately top with the crumb topping.
  • Use Room Temperature Ingredients –When the eggs are at room temperature they form an emulsion that helps to trap air and create the light, fluffy texture that’s so good.
  • Don’t Overbake – After 22 minutes be sure to test them with a toothpick, they get dry when overbaked!
  • Muffin liners make clean up easy but greasing the muffin tins with coconut oil works just as well. Let the muffins cool before removing from the pan.

Paleo Zucchini Chocolate Chip Muffins pan and hand holding

Crumb Topping

This is a simple topping to give the muffins a little extra texture. It’s optional but I love it!

Simply mix together blanched almond flour, coconut oil, maple sugar or coconut sugar. I used maple sugar in the photos, it has a lighter color.

The topping will probably seem soft when you first remove the muffins from the oven due to the coconut oil, but as they cool it will firm up to a crisp yummy crumble.

Paleo Zucchini Chocolate Chip Muffins pan with one taken out

Storage & Freezing Options For Zucchini Chocolate Chip Muffins

These muffins will store in the refrigerator in an airtight container for about 4 days. You’ll probably eat them all. But if you want to freeze some, place in an airtight container or sealable bag for up to 1 month.

I’ve made these muffins many times this summer. My family loves them.  Since zucchini are available year round you can make them all year long.  They’re nutritious, fluffy, tender, naturally sweetened, high protein and super satisfying.

If you like this recipe, try these other delicious healthy breakfast treats:

      Paleo Blueberry Muffins with Crumb Topping

      Amazing Paleo Pumpkin Muffins

      Paleo Morning Glory Bread

      Nut Free Banana Blueberry Bread

Would you like to have more of these delicious healthy recipes sent to you each week? CLICK TO SIGN UP for my weekly email newsletter of recipes and tips for you to eat well and enjoy your wonderful life.

Note: This post contains Amazon affiliate links. This means that if you click on a link and make a purchase, I will receive a small commission at no cost to you. As an Amazon Associate, I earn from qualifying purchases. Thank you for supporting Eat Well Enjoy Life.

clock clock iconcutlery cutlery iconflag flag iconfolder folder iconinstagram instagram iconpinterest pinterest iconfacebook facebook iconprint print iconsquares squares iconheart heart iconheart solid heart solid icon

Paleo Zucchini Chocolate Chip Muffins ( Gluten Free, Dairy Free)

5 Stars 4 Stars 3 Stars 2 Stars 1 Star

No reviews

  • Author: Ingrid DeHart
  • Total Time: 42 minutes
  • Yield: 12 muffins 1x


These muffins are beautifully moist, deliciously sweet and incredibly healthy. They’re high in protein, perfect for your morning breakfast or afternoon snack.



Topping (optional)


  1. Prepare the topping; Mix the almond flour, coconut sugar, coconut oil and salt together with a fork. It should look like crumbs. Chill while you prepare the batter.
  2. Shred your zucchini and squeeze out as much water as possible, you should have about 198 grams of zucchini after squeezing.
  3. Melt the coconut oil and let cool to room temperature.
  4. Preheat your oven to 350 degrees and line a muffin pan with parchment liners.
  5. In a medium bowl, combine the almond flour, arrowroot, baking soda and salt. Mix with a spoon or fork until evenly combined and there are no lumps.
  6. In a large bowl, use a fork to whisk together the eggs, almond butter, coconut oil, coconut sugar, vanilla and lemon juice until evenly combined.
  7. Stir the dry ingredients into the wet. The batter will be very thick at this point, that’s good since the zucchini will add lots of moisture to the batter.
  8. Fold the shredded and squeezed zucchini into the batter to distribute evenly.
  9. Stir in the chocolate chips. Save a few for the top if you like.
  10. Using a spoon, fill the muffin cups 3/4 of the way up, then cover the top of each muffin with the crumb topping. If desired top with a few chocolate chips.
  11. Bake in the preheated oven for 22-25 minutes or until lightly browned and a toothpick stuck in the center comes out clean.
  12. Allow muffins to cool in the pan for 10 minutes, then transfer to a wire rack to cool completely. Enjoy!


Maple sugar will give the muffins a lighter color.

  • Prep Time: 20 minutes
  • Cook Time: 22 minutes
  • Category: Breakfast, Snack
  • Method: Bake
  • Cuisine: Paleo, Gluten Free, Dairy Free, Refined Sugar Free

Rate & Comment

Your email address will not be published.

Recipe rating 5 Stars 4 Stars 3 Stars 2 Stars 1 Star