Healthy Zucchini Muffins

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Every year when zucchini come in season, these healthy zucchini muffins make an appearance at my house. this chocolate chip zucchini muffin recipe is sweet, moist, refined-sugar-free, and studded with melty chocolate. It’s the perfect balance of health and indulgence. Plus, they are the ideal complement to a brunch spread featuring a breakfast casserole, a refreshing fruit salad, classic easy peel eggs, and a steaming pot of freshly brewed coffee.

Zucchini is the perfect way to sneak veggies into recipes! I love mixing it into a batch of almond flour zucchini bread or fudgy zucchini brownies. It also offers so much flavor in savory dishes, like parmesan zucchini fries, hearty zucchini lasagna, and crispy zucchini chips, too. These zucchini muffins are just one more way to feed my obsession!

Healthy Zucchini Muffins Recipe: Why You’ll Love It

• Moist and tender texture
• Lightly sweet taste with a hint of cinnamon
• Melty chocolate chips
• No butter, oil, or refined sugar
• Naturally low carb, dairy-free, paleo, gluten-free, and grain-free
• Perfect for kids, breakfast, snacking, and meal prep

Ingredients & Substitutions

Here I explain the best ingredients for zucchini chocolate chip muffins, what each one does in the recipe, and substitution options. For measurements, see the recipe card.

• Wholesome Yum Coconut Flour – This is the brand I used to test this healthy zucchini muffin recipe, and it’s organic. Keep in mind that the moisture, consistency, and density of your coconut flour can greatly impact the outcome, because it’s so absorbent, so other brands might need more or less.
• Baking Powder – For optimal rising, use the freshest baking powder. Don’t confuse this with baking soda, which is not the same thing.
• Sea Salt
• Cinnamon – Adds a spiced flavor. You can also add a dash of nutmeg, allspice, or cardamom if you like.
• Honey – I used Wholesome Yum Zero Sugar Honey, but regular honey or even maple syrup works just as well.
• Eggs – I have not tested this recipe with any egg substitutes. It has a lot of eggs, which makes substitutions challenging, but it’s possible that 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 beverage or regular dairy milk if it fits your lifestyle.
• Zucchini – Use medium zucchini with firm skin. Use a box grater or food processor to shred it finely. You’ll need 2 cups of shreds, which is about 3 medium zucchini.
• Chocolate Chips – To keep these muffins healthier, I use sugar free chocolate chips instead of regular, but any kind will work.

VARIATION: Add other mix-ins!

To customize your muffins, feel free to omit chocolate chips, and add chopped nuts, seeds, or even dried cranberries instead. However, be mindful to only include add-ins that are either very concentrated or dry pieces to avoid altering the batter consistency.

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 with amounts and temperatures, see the recipe card.

1. Prep. Preheat the oven and line a muffin pan with parchment paper liners. 
2. Whisk the dry ingredients. In a large bowl, whisk together the coconut flour, baking powder, salt, and cinnamon.
3. Mix the wet ingredients. In a separate bowl, whisk together honey, eggs, vanilla and almond milk.
4. Combine. Add the wet ingredients to the dry ingredients, and whisk or stir just until combined.

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

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

Notes About These Zucchini Muffins

These healthy zucchini muffins are pretty easy to make, but here are some surprising aspects to making them:

• You don’t need to squeeze zucchini. Because these muffins are made with coconut flour, which is very absorbent, there is no need to squeeze the shredded zucchini. If the zucchini feels wet, gently pat with paper towels.
• The batter will look a little dry. Although I’ve increased the liquid in this recipe, coconut flour is strange in that it makes the batter look drier than it actually is. Resist the urge to add more liquid, or the muffins will be wet.
• Fill the batter to the top. Zucchini muffins with coconut flour don’t rise very much, so you need to fill the muffin liners pretty full.

Storage Instructions

• Store: You can keep chocolate chip zucchini muffins on the counter for a couple days, or place in an airtight container and store in the fridge for up to 1 week.
• Reheat: If you like your healthy chocolate zucchini muffins warm when you eat them, simply heat them in the microwave for 15-30 seconds. You can also warm them up in the oven at 325 degrees F for a few minutes.
• Freeze: Cool muffins completely, then place in a freezer bag and freeze for up to 3 months. Some people prefer to let them freeze in the muffin tin first, then transfer to a bag when solid, to ensure they don’t get crushed. Thaw on the counter or in the fridge overnight before reheating in the oven or microwave.

More Healthy Muffin Recipes

I love customizing the flavor in muffins — without the extra junk. Try some of my favorite recipes:

Healthy Banana Muffins

Chocolate Protein Muffins

Coconut Flour Blueberry Muffins

Keto Blueberry Muffins

Recipe Card

4.5 from 34 votes

Healthy Zucchini Muffins (Chocolate Chip)

By Maya Krampf

Sneak veggies into your breakfast with this healthy zucchini chocolate chip muffins recipe. They're perfectly moist with melty chocolate!

Prep: 15 minutes

Cook: 30 minutes

Total: 45 minutes

Servings: 12 (adjust to scale recipe)

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Ingredients

[ See substitutions ]

U.S. – Metric

Tap underlined ingredients to see the ones I use.

• 3/4 cup Wholesome Yum Coconut Flour ▢
• 2 tsp Baking powder ▢
• 1/4 tsp Sea salt ▢
• 1/2 tsp Cinnamon ▢
• 1/2 cup Wholesome Yum Zero Sugar Honey (or regular honey) ▢
• 6 large Eggs ▢
• 1/2 tsp Vanilla extract ▢
• 1/4 cup Unsweetened almond milk ▢
• 8 oz Zucchini (shredded/grated, about 2 cups) ▢
• 1/2 cup Sugar-free dark chocolate chips ▢

Instructions

[ See step photos ]

Tap on the times in the instructions to start a kitchen timer.

1. Preheat oven to 350 degrees F (177 degrees C) and line a muffin tin with parchment paper liners.

2. In a large bowl, whisk together the coconut flour, baking powder, salt and cinnamon.

3. In a separate large bowl, whisk together the honey, eggs, vanilla and almond milk.

4. Add the wet ingredients to the dry ingredients and whisk just until combined.

5. Fold in the shredded zucchini and chocolate chips.

6. Transfer the batter to the prepared muffin tins. Fill all the way to the top.

7. Bake zucchini muffins for 28-30 minutes, until golden brown on top and a toothpick inserted into the center of a muffin comes out clean.

8. Remove from oven and let cool 15 minutes before serving.

Did you make it? Leave a review or tag me @wholesomeyum on Instagram!

Maya’s Recipe Notes

Serving size: 1 muffin

Nutrition Facts

Amounts per serving. Serving size in recipe notes above.

Calories 124

Fat 7g

Protein 4.5g

Total Carbs 14.9g

Net Carbs 3.2g

Fiber 11.7g

Sugar 1.1g

I provide nutrition facts as a courtesy. Have questions about calculations or why you got a different result? Please see my nutrition policy.

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Try More Of My Recipes

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  Zucchini Brownies
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