Healthy Zucchini Muffins (Chocolate Chip) - Wholesome Yum (2024)

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

This section explains how to choose the best ingredients for zucchini chocolate chip muffins, what each one does in the recipe, and substitution options. For measurements, see the recipe card below.

• 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.

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 the recipe card below.

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.

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: