Healthy Chocolate Zucchini Muffins

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These Healthy Chocolate Zucchini Muffins are perfect year round, but especially in the summer when there’s tons of zucchini! They’re perfectly moist, fudgy, and both freezer and kid friendly too. They’re made with almond flour, naturally gluten free and paleo as well.

Paleo Chocolate Zucchini Muffins | Get Inspired Everyday!

Are you looking for recipes to use zucchini? I sure hope so because these chocolate-y muffins are perfect for that. I planted 4 zucchini plants this summer, so I’m prepared to be overrun about halfway through July. But for now, I’m just super excited about the little tiny zucchini already growing!

We also did a CSA this year from our favorite local farmer, so I’m expecting way more zucchini than we’ve ever had around before. (A CSA is where you prepay for a season’s worth of veggies, and sometimes fruit depending on where you live and the program.)

So if you’re about to be overrun too, definitely check out some of my favorite ways to use zucchini below. And this year I’m also putting together a post featuring zucchini, so stay tuned for that. And if you’re really loving muffins right now, try my Paleo Pineapple Zucchini Muffins as well.

Gluten Free Chocolate Zucchini Muffins perfect for zucchini season!

But back to these muffins! They’re fudgy, deeply chocolate-y, and perfectly moist as you might expect from the grated zucchini in there. I added chocolate chips too because like my mom always says, ‘you can’t have too much chocolate’. And you can see by their crackly tops, the texture is on point!

These muffins also freeze really well, and they’re great to have around when you need something grab-and-go. They only thing with taking them straight out of the freezer is they do loose the crispness factor in the tops. You can also get that back by gently reheating them in the oven. But it’s a small price to pay to have something so tasty, ready-to-go at a moments notice.

Let’s make this recipe step by step

Batter texture for my Paleo Chocolate Zucchini Muffins!

First up mix the dry ingredients before adding the wet ingredients. The batter is on the looser side, just slightly thicker than cake batter normally is.

Prepped into muffin cup liners for easy cleanup!

Then you portion them out evenly into a lined muffin tin and…

These chocolate muffins are fudgy with lovely crackled tops!

… bake just until the tops are crackly and they’re puffed in the middle. A toothpick inserted into the center will come out mostly clean with a few fudgy crumbs. You don’t want to see raw batter, that means they still need a few minutes.

Paleo Chocolate Zucchini Muffins | Get Inspired Everyday!

From there it’s time to carefully remove them from the muffin tin to fully cool on a cooling rack. You can eat them hot or warm straight out of the oven. But I think they get even more chocolate-y after they’ve cooled to room temperature.

More almond flour muffin recipes

Gluten Free Chocolate Zucchini Muffins!

5 favorite zucchini recipes

I sure hope you’ll enjoy these muffins as much as we have! If you do make them, I hope you’ll leave me a comment/rating below. And I always love hearing from you here. Or over on Instagram where you can tag me at #getinspiredeveryday with your photos.

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Paleo Chocolate Zucchini Muffins | Get Inspired Everyday!

Healthy Chocolate Zucchini Muffins

  • Author: Kari Peters
  • Total Time: 45 minutes
  • Yield: 12 1x
  • Diet: Gluten Free


These fudgy muffins are perfectly moist thanks to the zucchini, and have extra chocolate flavor with the chocolate chips added in!



1 1/2 cups fine almond flour

1/2 cup tapioca starch

1/2 cup cocoa powder

2 Teaspoons baking powder, see notes

1/2 Teaspoon salt

1/2 cup mini chocolate chips, see notes

1 1/2 cups grated zucchini, lightly squeezed to remove excess water

1/3 cup avocado oil

1/2 cup maple syrup

2 eggs

1 Tablespoon vanilla extract


Preheat the oven to 350ºF and line a muffin tin with muffin cup liners.

In a medium sized mixing bowl, combine the almond flour, tapioca starch, baking powder, and sea salt.

Stir in the chocolate chips, then fold in the zucchini.

Then add the avocado oil, maple syrup, eggs, and vanilla extract. Mix just until combined, then evenly portion the batter out into the muffin cups. The muffin cups will be quite full but don’t worry, they don’t rise too much.

Bake until the muffins are puffed in the center, and a toothpick inserted into the center comes out with just moist crumbs, no batter, about 20-25 minutes.

Let the muffins cool for 5-10 minutes on a cooling rack before carefully removing them.

Serve, or wait for them to cool completely for the deepest chocolate flavor.

Any leftovers can be frozen, then reheated gently at 150ºF until heated through.


Baking powder can have all sorts of additives, and isn’t always gluten free or paleo. To be safe, you can make your own by mixing together 1 part baking soda to 2 parts cream of tartar, and use the mixture right away.

I use Enjoy Life chocolate chips because they’re allergy friendly, and also super tasty!

  • Prep Time: 20
  • Cook Time: 25
  • Category: Baking
  • Method: Mixing
  • Cuisine: American

Keywords: Zucchini Muffins, Chocolate Zucchini Muffins, Gluten Free Chocolate Zucchini Muffins, Paleo Zucchini Muffins, Healthy Chocolate Zucchini Muffins

2 thoughts on “Healthy Chocolate Zucchini Muffins”

  1. Hi! Looking so forward to trying this recipe!! Do you think you could replace the eggs with applesauce or egg replacer? I’m allergic to eggs:(

    Thanks so much!

    • I wouldn’t go with applesauce as a substitute here for eggs because the zucchini already adds a lot of moisture. I would try a ‘flax egg’ mixing water and ground flax together instead if you can. The ratio for a flax egg are 1 tablespoon ground flax to 2.5 tablespoons of water. Mix them together and let sit for 10 minutes before using. I hope this helps, and be sure to let me know how it goes, or if you have any more questions!


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