Healthy Chocolate Zucchini Muffins

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Fluffy, fudgy, and perfectly moist these Healthy Chocolate Zucchini Muffins are the perfect way to use zucchini. These muffins are the perfect chocolate treat, like healthy cupcakes. But they’re healthier thanks to that hidden grated zucchini. Made with real food ingredients like almond flour they’re naturally gluten-free. They’re naturally sweetened with maple syrup as well rather than refined sugar which also helps them to stay moist.

Side view of Gluten Free Chocolate Zucchini Muffins on a wooden board with chocolate chips scattered around them.

With abundant summertime zucchini in full swing, I start adding zucchini to almost everything I make. We often eat it as a side dish for dinner, but I also love baking with zucchini.

Zucchini adds just the right ‘moist’ factor to baked goods. And it makes these chocolate muffins extra fudgy in combination with chocolate chips.

If you’re also overrun with zucchini right now, check out my 35 Healthy Zucchini Recipes to help you use it up. And if you’re looking for more baked goods to try, my Pineapple Zucchini Muffins, Lemon Zucchini Cake, or Zucchini Blueberry Bread are favorites in our house.

Paleo Chocolate Zucchini Muffins on a wood cutting board with chocolate chips scattered around them and one muffin broken in half.

Ingredients & Substitutions

All the ingredients for Healthy Chocolate Zucchini Muffins: almond flour, tapioca starch, cocoa powder, zucchini, vanilla, baking powder, chocolate chips, maple syrup, eggs, avocado oil, and salt in bowls on a wood cutting board.
  • Almond Flour & tapioca starch – are combined together as the flour in this recipe. The almond flour provides wonderful flavor and moisture. And the tapioca starch helps to hold the almond flour together and produce a fluffy muffin.
  • Cocoa powder – also provides structure to these muffins, but more importantly, it’s the main source of chocolate flavor.
  • Baking Powder – provides rise and lightness to these muffins. There is an alternative listed in the recipe notes if needed.
  • Zucchini – grated or shredded zucchini adds the perfect moistness and hidden vegetables.
  • Maple syrupGrade A amber is my favorite flavor pairing with the chocolate, but honey does work as well.
  • Eggs – bind these muffins together and help to create a fluffy texture.
  • Avocado oilor neutral-tasting cooking oil both work and keep these muffins dairy-free. Melted butter, ghee, or coconut oil also work in these muffins.
  • Chocolate chips – I like to add mini chocolate chips for an extra chocolate boost, but you can omit them if desired. Adding chocolate chips makes these muffins more love a treat because they’re double chocolate zucchini muffins.

How to make this recipe step by step

Mixing together the dry ingredients for the healthy chocolate zucchini muffins in a large white bowl on a wood cutting board.

Step 1: Begin by preheating the oven and mixing together the dry ingredients in a large mixing bowl.

Mixing the grated zucchini into the dry ingredients for the almond flour chocolate zucchini muffins.

Step 2: Grate the zucchini and add it to the dry ingredients. Stir to combine and coat the zucchini with the flour mixture.

You don’t need to squeeze the water out of the zucchini for this recipe. I formulated it specifically to skip that extra step!

Mixing the wet ingredients into the large white bowl to form the batter for the healthy chocolate zucchini muffins.

Step 3: Add the wet ingredients and stir until a batter forms and no pockets of the flour mixture remain.

Portioning out the batter for chocolate zucchini muffins into a muffin tin with liners.

Step 4: Portion the muffin batter into a muffin pan lined with muffin liners, (sometimes called cupcake liners). I use 2 spoons to portion it out, but you can also use a large cookie scoop.

Freshly baked healthy chocolate zucchini muffins still in the muffin tin.

Step 5: Bake until the muffins are puffed in the centers and a toothpick inserted comes out clean or with moist crumbs.

Removing the healthy chocolate zucchini muffins from the muffin tin onto a wire cooling rack.

Step 5: When the muffins are done allow them to cool enough to remove from the muffin tin and place on a wire rack to finish cooling.

Serve warm with butter or cool to room temperature for the deepest chocolate flavor.

Healthy Chocolate Zucchini Muffins on a wood cutting board with chocolate chips scattered around them.

Ways to serve this

  • Serve these fresh and warm right out of the oven with butter. They’re also great at room temperature with even more chocolate flavor as they cool to room temperature.
  • Add these to the table for a larger breakfast or brunch with my Sausage Hash Brown Breakfast Bake or Veggie Breakfast Casserole (which also uses zucchini).
  • Or keep it simple and serve these chocolate zucchini muffins with my Turkey Breakfast Sausage and scrambled eggs.


Can I use gluten-free flour instead of almond flour?

No, gluten-free flour doesn’t work as a substitute for almond flour. Almond flour adds a lot of moistness to the muffins and gluten-free flour would cause the muffins to be very dry. I have a gluten-free banana bread recipe you could try making instead which uses gluten-free flour.

What can I use instead of zucchini for these muffins?

I don’t recommend subbing in anything for the zucchini. Instead try making my Pumpkin Muffins, Apple Muffins, or Banana Muffins.

Storing leftovers

  • To store – cool the muffins to room temperature and store them in an airtight container on the counter for up to 2 days. The muffins will begin to dry out over time, so I freeze any leftovers I have right away.
  • Make ahead – These muffins can be made ahead and frozen. Defrost them overnight in the fridge or on the counter and reheat slightly to serve.
  • Reheating – place the muffins in an oven or toaster oven at 250ºF for 10 minutes or so until heated through. Or you can also microwave to reheat.
  • To freeze – these keep well in an airtight container in the freezer for up to one month. Be sure to let them cool to room temperature before freezing.
Close up straight down view of paleo chocolate zucchini muffins on a wood cutting board.

Tips & Tricks

  • If you’re serving any picky eater (especially kids) try peeling the zucchini before you grate it so there are no green bits. Most picky eaters don’t even notice a fleck of green here or there in these fudgy chocolate muffins. But if you’re struggling with the color green in food, peeling the zucchini is a good first step!
  • If you want to make these muffins free of refined sugar, omit the chocolate chips. There’s still plenty of chocolate flavor to go around. We always include chocolate chips in our house but only because we can never get enough chocolate! Try Enjoy Life chocolate chips for allergy-friendly chocolate chips, (plus they taste really good!).
Further out straight down view of healthy chocolate zucchini muffins on a wood cutting board with mini chocolate chips around them and one muffin broken in half.

I really hope you enjoy these Healthy Chocolate Zucchini Muffins! If you do get a chance to make this recipe, I’d love to hear from you in the comments.

Healthy Chocolate Zucchini Muffins on a wood cutting board with chocolate chips scattered around them.

Healthy Chocolate Zucchini Muffins

5 from 2 votes
Author: Kari Peters
Total Time 45 minutes
Yield: 12 muffins
Course: Baking


  • 1 1/2 cups fine almond flour
  • 1/2 cup tapioca starch
  • 1/2 cup cocoa powder
  • 2 tsp baking powder - see notes
  • 1/2 tsp salt
  • 1/2 cup mini chocolate chips - see notes
  • 1 1/2 cups grated zucchini
  • 1/3 cup avocado oil
  • 1/2 cup Grade A amber maple syrup
  • 2 eggs
  • 1 tbsp 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, cocoa powder, baking powder, and sea salt.
  • Stir in the chocolate chips, then fold in the grated zucchini.
  • Next 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, the rise will be just right.
  • 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 and placing them on a cooling rack.
  • Serve right away, 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.
Bonus StepIf you made this recipe, please leave a rating/comment. Ratings really help us continue to bring you high-quality free recipes. Rate This Recipe!


Baking powder can contain 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!
Category: Baking
Cuisine: American
Keywords: Almond Flour Zucchini Muffins, Chocolate Zucchini Muffins, Gluten Free Chocolate Zucchini Muffins, Paleo Chocolate Zucchini Muffins, Paleo Zucchini Muffins

nutrition facts

Serving: 1muffin | Calories: 248kcal | Carbohydrates: 24g | Protein: 5g | Fat: 16g | Saturated Fat: 3g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 5g | Trans Fat: 0.02g | Cholesterol: 28mg | Sodium: 186mg | Potassium: 138mg | Fiber: 3g | Sugar: 14g | Vitamin A: 87IU | Vitamin C: 3mg | Calcium: 103mg | Iron: 1mg
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This recipe was originally published in 2020 and updated in 2023 with more tips and information.

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!

5 from 2 votes (2 ratings without comment)

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