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Every year when zucchini is on the market, these Healthy Zucchini Muffins Show up at my house. This Chocolate Chip Zucchini Muffin recipe is sweet, moist, refined and sugar-free, and studded with melted chocolate. It’s the perfect balance of healthy and indulgent.
Zucchini is the perfect way to incorporate vegetables into a recipe!I like to mix it up in a batch Almond Flour Zucchini Bread or fudge Zucchini Brownies.It also lends a rich flavor to savory dishes like Parmesan Zucchini Frieshearty Zucchini Lasagnaand crispy zucchini slices, also. These Zucchini Muffins are just another way to satisfy my obsession!
Healthy Zucchini Muffins Recipe: Why You’ll Love It
- Moisturizing and soft texture
- Lightly sweet with a hint of cinnamon
- melted chocolate chips
- No Butter, Oil or Refined Sugar
- Naturally Low Carb, Dairy Free, Paleo, Gluten & Grain Free
- great for kids, breakfastsnacks and meal prep

Ingredients and Substitutes
This section explains how to choose the best ingredients for Zucchini Chocolate Chip Muffins, the role each ingredient plays in the recipe, and substitution options.For measurements, see recipe card below.
- Wholesome Delicious Coconut Flour – This is the brand I used to test the healthy zucchini muffin recipe, and it’s organic. Keep in mind that the moisture, consistency and density of coconut flour can greatly affect the results, as it is very absorbent, so other brands may need more or less.
- baking powder – For best leavening results, use the freshest baking powder available. Don’t confuse it with baking soda, they are not the same thing.
- sea salt
- Cinnamon – Add spices for flavor. You can also add a dash of nutmeg, allspice or cardamom if you like.
- Honey – I used Wholesome Yum Zero Sugar Honeybut regular honey and even maple syrup have the same effect.
- Egg – I haven’t tested this recipe with any egg substitute.It has a lot of eggs, which makes the substitution challenging, but possible flax eggs might work.
- vanilla extract – Use high quality vanilla extract for the best flavor.
- almond milk – make your own Homemade Almond Milk, or use unsweetened store-bought milk. You can also use other types of milk, such as coconut milk drinks or regular milk, if it suits your lifestyle.
- zucchini – Use medium-sized zucchini with firm skin. Shred it using a box grater or food processor. You’ll need 2 cups shredded, which is about 3 medium zucchini.
- chocolate chips – To make these muffins healthier, I use Sugar Free Chocolate Chips instead of regular, but any type will do.
Variations: Add other remixes!
To customize your muffins, feel free to omit the chocolate chips and add chopped nuts, seeds, or even dried cranberries instead. However, be careful to only add very concentrated or dry additional ingredients to avoid changing the consistency of the batter.

How to Make Healthy Zucchini Muffins
This section shows how to make zucchini muffins, with step-by-step photos and details about the technique to help you visualize it.For full instructions, including amounts and temperatures, see recipe card below.
- Prepare. Preheat oven and line muffin pan and parchment liner.
- Stir in dry ingredients. In a large bowl, whisk together coconut flour, baking powder, salt, and cinnamon.
- Mix wet ingredients. In another bowl, whisk together honey, eggs, vanilla extract, and almond milk.
- combined. Add the wet ingredients to the dry ingredients and whisk or whisk until combined.


- Add zucchini. Stir in grated zucchini and chocolate chips. Transfer batter to prepared muffin tins. Fill to the top.


- bake. Pop healthy zucchini muffins in the oven. Bake until golden brown on top and a toothpick inserted into the center comes out clean.
- cool. Remove from oven and let cool on a wire rack before serving.

Notes About These Zucchini Muffins
These healthy zucchini muffins are easy to make, but there are some surprising aspects to making them:
- You don’t need to squeeze the zucchini. Since these muffins are made with coconut flour, which is super absorbent, there’s no need to squeeze the shredded zucchini. If the zucchini feels soggy, pat it lightly with a paper towel.
- The batter will look a little dry. Although I increased the liquid in this recipe, the coconut flour was weird because it made the batter look drier than it really was. Resist the urge to add more liquid or the muffins will be soggy.
- Fill with batter. Zucchini muffins with coconut flour won’t expand much, so you’ll need to fill the muffin liners.
storage instructions
- shop: You can keep Chocolate Chip Zucchini Muffins on the counter for a few days, or store in an airtight container in the refrigerator for up to 1 week.
- Reheat: If you like your healthy chocolate zucchini muffins served hot, just pop them in the microwave for 15-30 seconds. You can also pop them in a 325°F oven for a few minutes.
- freeze: Cool muffins completely, then place in freezer bags and freeze for up to 3 months. Some people like to freeze them in muffin tins first, then transfer to bags after they’ve set to make sure they don’t get crushed. Thaw overnight on the counter or in the refrigerator, then reheat in the oven or microwave.

Healthier Muffin Recipes
I love the taste of custom made muffins – no extra crap. Try some of my favorite recipes:
Healthy Zucchini Muffins (Chocolate Chip)
Incorporate veggies into your breakfast with this healthy Zucchini Chocolate Chip Muffins recipe. They were perfectly moistened with melted chocolate!
Prepare: 15 minute
chef: 30 minute
all: 45 minute
Serving Size: 12 (Adjust according to recipe ratio)
raw material
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instruct
Click on the time in the instructions below to start the kitchen timer while cooking.
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Preheat oven to 350°F (177°C) and line muffin tin and parchment liner.
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In a large bowl, whisk together coconut flour, baking powder, salt, and cinnamon.
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In another large bowl, whisk together honey, eggs, vanilla extract, and almond milk.
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Add wet ingredients to dry ingredients, stirring until combined.
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Stir in the chopped zucchini and chocolate chips.
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Transfer batter to prepared muffin tins. Fill all the way to the top.
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Baked Zucchini Muffins 28-30 minutesuntil golden brown on top and a toothpick inserted into center of muffin comes out clean.
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Remove from oven and let cool 15 minutes before serving.
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recipe notes
Serving Size: 1 muffin
nutrient content
Amount per serving. Serving sizes in recipe instructions above.
calories 106
fat 5.7 grams
protein 5.5 grams
total carbohydrates 12.3 grams
net carbs 3.6 grams
fiber 8.7 grams
sugar 1.1 grams
Nutrition Facts are provided as a courtesy. Questions about calculations or why do I get different results?Please view our nutrition policy.
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