These chocolate and zucchini muffins combine rich double chocolate flavor with incredibly moist texture, all while sneaking in two cups of vegetables that you can’t even taste! What makes our recipe special is the thoughtful blend of whole wheat flour, ground flax, and hidden zucchini that adds fiber, protein, and nutrients without sacrificing any of the indulgent chocolate flavor. Ready in just 35 minutes, these muffins are wholesome enough for breakfast yet satisfying enough for dessert.
As a self-proclaimed chocoholic, I’ve always had a soft spot for those double chocolate chip muffins from my childhood. Those were such a special treat growing up, and I wanted to recreate that same rich, chocolatey experience but in a way that felt better for everyday eating. Having developed over 40 breakfast recipes for this website, I’ve spent years perfecting ways to make classic treats more nutritious without compromising on taste. I absolutely love baking with zucchini because of its ability to add moisture and nutrition to your baked good while remaining completely undetectable.
I love that these muffins solve the challenge of wanting something sweet and satisfying while still getting good nutrition. The combination of cocoa powder and chocolate chips delivers serious chocolate flavor that satisfies my chocolate cravings, while the zucchini, whole wheat flour, and ground flax boost the nutritional value significantly. Whether you’re looking for a special breakfast treat, an after-school snack, or a way to use up garden zucchini, these muffins deliver on all fronts.
Love baking with zucchini too? Be sure to try our easy zucchini muffins with applesauce and whole wheat zucchini bread with chocolate chips too! Or go savory and try our zucchini fritters or our crustless zucchini quiche.
Jump to:
- Why You’ll Love This Chocolate and Zucchini Muffins Recipe
- Ingredients for Chocolate Muffins with Zucchini
- Zucchini Chocolate Muffins Step-By-Step Instructions
- Double Chocolate Chip Zucchini Muffins Variations
- Expert Tips on Grating Zucchini
- Storing Chocolate and Zucchini Muffins
- Information on Ground Flax
- Healthy Chocolate Zucchini Muffins FAQs
- Love This Recipe? Try One of These Muffin Recipes Next!
- Healthier Double Chocolate Zucchini Muffins
Why You’ll Love This Chocolate and Zucchini Muffins Recipe
Ready in Just 35 Minutes. Quick prep and baking time makes these perfect for when you want fresh, homemade muffins without spending all day in the kitchen.
Sneaky Nutrition Boost. Packed with wholesome ingredients like whole wheat flour, ground flax, and 2 cups of hidden zucchini that add fiber, protein, and nutrients without sacrificing taste.
Incredibly Moist and Chocolatey. The hidden zucchini creates ultra-moist texture while cocoa powder and chocolate chips deliver rich, double chocolate flavor in every bite.
Perfect for Any Time of Day! Great for breakfast, snack time, or dessert, these muffins satisfy your chocolate craving while being wholesome enough to enjoy anytime.
Ingredients for Chocolate Muffins with Zucchini
- Granulated sugar and brown sugar. Provide sweetness and moisture, with brown sugar adding extra richness and helping create the tender muffin texture.⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
- Vegetable oil. Ensures these muffins turn out moist and tender every time with a soft, bakery-style texture.⠀⠀⠀⠀⠀⠀⠀⠀
- Large eggs. Helps to bind the ingredients together, add structure, add richness, and contribute to the moist texture.⠀⠀⠀⠀⠀⠀⠀
- Vanilla extract. Enhances the chocolate flavor and adds warmth that complements all the other ingredients.⠀⠀⠀⠀⠀⠀⠀⠀⠀
- Ground flax. One of my favorite ingredients to add into muffins, ground flax adds fiber, protein, and omega-3 fatty acids for extra nutrition without affecting the taste.⠀⠀⠀⠀⠀
- Zucchini. The secret ingredient that adds incredible moisture and sneaks vegetables into your muffins (without any veggie taste!).⠀⠀⠀⠀⠀⠀⠀⠀
- Salt, Baking Soda, and Cinnamon. Essential for proper rise, flavor balance, and a touch of warm spice that enhances the chocolate.⠀⠀⠀⠀
- Cocoa powder. Provides rich chocolate flavor and that beautiful dark color, making these truly double chocolate muffins.⠀⠀⠀⠀
- All-Purpose Flour and Whole Wheat Flour. Used in the perfect ratio to create an excellent muffin structure while whole wheat flour adds extra fiber, protein, and nutrients too.⠀⠀⠀⠀⠀
- Chocolate chips. Add bursts of melty chocolate throughout every muffin for extra indulgence! We use semi-sweet, but you can play around with the type of chocolate chips you like best!
- Optional: mini-chocolate chips for topping. Perfect for sprinkling on top to make these muffins look bakery-beautiful and add extra chocolate in every bite.
See the recipe card at the bottom of the page for all ingredient measurements and recipe directions.
Choosing and Measuring Zucchini
Selecting the Best Zucchini: If possible, choose medium-sized zucchini (about 6-8 inches long) for the best flavor and texture. Avoid very large zucchini (like those baseball bat sized ones that hid in the garden too long…) as they can be watery and have tough seeds. Look for zucchini that feel firm and heavy for their size with smooth, unblemished skin.
Measuring Grated Zucchini: When measuring your 2 cups of grated zucchini, pack it loosely into the measuring cup. Don’t press it down or compact it. There’s no need to squeeze out excess liquid; the moisture actually helps create incredibly moist muffins, which is exactly what we want!
Zucchini Chocolate Muffins Step-By-Step Instructions
Preheat oven & prep your muffin tins: Preheat your oven to 350°F, then spray muffin tins with non-stick cooking spray and set aside.
Make the muffin batter by first adding the sugars and wet ingredients to a large mixing bowl.
Whisk to combine.
Add the grated zucchini into the bowl with the wet ingredients.
And stir to combine (switching over to a rubber scrapper).
Gradually add in dry-ingredients, stirring until about 75% combined (you’ll still see flour streaks).
Add the chocolate chips to the bowl.
Gently stir until JUST combined (a few lumps in the batter are ok! Don’t over mix).⠀⠀
Transfer the batter to the prepared muffin tins, filling each cup about ¾ full.
Sprinkle the top of the muffins with mini chocolate chips if desired.
Bake: Bake 18-22 minutes, or until a toothpick comes out clean. Cool in tin for about 5 minutes, then remove muffins and place on a wire rack to finish cooling.
Time Saving Tip
It can take a little while to grate your zucchini, especially if you’re doing it by hand (which is my preferred method). If you want to shave some time off this recipe, use the grating attachment on a food processor to make quick work of this step.
Double Chocolate Chip Zucchini Muffins Variations
Natural Sweetener Substitutions: You can replace the granulated sugar with natural alternatives, though I haven’t tested these in this specific recipe. When using liquid sweeteners, reduce the oil by 3-4 tablespoons to maintain proper texture.
- Unsweetened applesauce: 1-to-1 ratio (my preferred swap – replace only the granulated sugar, keep the brown sugar)
- Honey: ¾ cup honey for 1 cup granulated sugar
- Maple syrup: ¾ cup maple syrup for 1 cup granulated sugar
- Agave: ⅔ cup agave for 1 cup granulated sugar
If your batter seems too thin after making substitutions, add 1-2 extra tablespoons of flour until you reach the right consistency.
Possible Dietary Restrictions?
If desired, you can make this recipe gluten free! To do so, replace both the all-purpose flour and whole wheat flour with the same total amount (2.5 Cups) of a good quality 1-to-1 gluten-free flour blend. This change may result in slightly more dense or crumbly muffins, but the zucchini and oil should help maintain the muffin’s moisture.
If serving to someone with celiac, be sure to double check the labels on your other ingredients (especially the chocolate chips!) to ensure they’re certified gluten-free.
Expert Tips on Grating Zucchini
A few tips for grating zucchini include:
TIP 1: After washing your zucchini, cut off the rounded end and use the stem-end as a handle.
TIP 2: I like to use a simple 3D, or box grater, to grate my zucchinis. I place my grater on a dinner plate, and while applying medium pressure, quickly move the zucchini up and down the face of the grater while always keeping the zucchini touching the grater (it grates on the downward motion). The box grater keeps most of the zucchini pieces inside of it, and the plate is a simple surface to transfer your grated zucchini over to a measuring cup on and then to clean afterwards.
TIP 3: Don’t select a super small grating size for zucchinis, they will turn to mush. I use the larger, circular holes on my box grater. Similar to what you might use for a block of cheese.
Storing Chocolate and Zucchini Muffins
Store cooled double chocolate zucchini muffins in an air-tight container for up to 3 days at room temperature or up to 1 week in the refrigerator.
Freezer Option
You can also freeze these muffins for up to 3 months! To do so, once the muffins have completely cooled, wrap individual muffins in plastic wrap and place into a labeled zip-top storage bag or place into a freezer-safe container. Thaw the muffins at room temperature or warm briefly in the microwave when ready to enjoy.
Information on Ground Flax
If you’re new to using ground flaxseed, you may be wondering how to store this ingredient properly and other ways you can use it. Here I’ve outlined best practices for storage and other ways I use flax in my house (which is a lot!).
Storing Ground Flaxseed
Ground flax should be stored in an air-tight container in the fridge or freezer. This helps prevent your flaxseed from going rancid.
Flax will stay fresh for up to 6 months when stored in the fridge, and up to 1 year when stored in the freezer. You can simply place your closed package of ground flax in a gallon sized ziplock bag with the air squeezed out, or transfer it to a different container with a lid – whatever is easiest for you!
How Else Can I Use Ground Flax?
You can use ground flax in so many ways to add nutrition to your meals. Below are a few of my favorite ways to use ground flax.
- Like this double chocolate zucchini muffin recipe, I add ground flax into most of my breakfast bakes. It’s in my whole wheat zucchini bread recipe, and I love adding it into pancakes and waffles too!
- Add it to smoothies! I always toss a generous scoop into this cherry berry smoothie or this easy green smoothie.
- Sprinkle on top of oatmeal or cereal.
- Add them to your homemade no-bake energy bites or homemade granola bars.
- Create a “flax egg” in baking recipes as an egg substitute (this has come in handy when I’ve been out of eggs!). This is done by using 1 tablespoon of flax to 3 tablespoon of water.
Healthy Chocolate Zucchini Muffins FAQs
Yes! Since you’re already doubling-down on the chocolate, why stop? The mini chocolate chips on the top really add to the overall double chocolate muffin experience in my opinion, so I would say you should go for it!
Yes! You can simply omit the ground flax if you don’t have it on hand. Since flax absorbs some liquid, you may want to add an extra tablespoon or two of flour to maintain the proper batter consistency (see how it looks after adding the dry ingredients). The muffins will still be delicious and moist, you’ll just miss out on the extra fiber, protein, and omega-3s that flax provides.
You can replace the whole wheat flour with an equal amount of all-purpose flour. The muffins will be just as delicious, though you’ll miss out on some of the extra fiber and nutrients that whole wheat provides.
Yes! You can substitute the vegetable oil with canola oil or melted butter. You can also use melted coconut oil (cooled slightly), but I find it changes the flavor a bit. Each option will give slightly different results, but all will create moist, tender muffins.
Love This Recipe? Try One of These Muffin Recipes Next!
Healthier Double Chocolate Zucchini Muffins
Ingredients
- 1 Cup granulated sugar⠀⠀⠀⠀⠀⠀⠀⠀⠀
- ⅔ Cup brown sugar⠀⠀⠀⠀⠀⠀⠀⠀⠀
- 1 Cup vegetable oil⠀⠀⠀⠀⠀⠀⠀⠀⠀
- 3 large eggs⠀⠀⠀⠀⠀⠀⠀⠀⠀
- 1 Tablespoon vanilla⠀⠀⠀⠀⠀⠀⠀⠀⠀
- 2 Tablespoon ground flax⠀⠀⠀⠀⠀⠀⠀⠀⠀
- 2 Cup grated zucchini⠀⠀⠀⠀⠀⠀⠀⠀⠀
- 1 teaspoon salt⠀⠀⠀⠀⠀⠀⠀⠀⠀
- 1 teaspoon baking soda⠀⠀⠀⠀⠀⠀⠀⠀⠀
- 1 teaspoon cinnamon⠀⠀⠀⠀⠀⠀⠀⠀⠀
- ½ Cup cocoa powder⠀⠀⠀⠀⠀⠀⠀⠀⠀
- 1.5 Cup all-purpose flour⠀⠀⠀⠀⠀⠀⠀⠀⠀
- 1 Cup whole wheat flour⠀⠀⠀⠀⠀⠀⠀⠀⠀
- 1 Cup chocolate chips⠀⠀⠀⠀⠀⠀⠀⠀⠀
- Optional: mini-chocolate chips for topping (about ⅓ Cup)
Instructions
- Preheat oven to 350°F, coat muffin tins with non-stick cooking spray and set aside⠀⠀⠀⠀⠀⠀⠀⠀⠀
- In a large bowl, mix together sugars, oil, eggs, and vanilla until well combined
- Add in zucchini and stir to combine
- Gradually add in dry-ingredients until just combined. Gently stir in chocolate chips⠀⠀⠀⠀⠀⠀⠀⠀⠀
- Fill muffin tins ¾ full. Option to sprinkle with mini chocolate chips if desired⠀⠀⠀⠀⠀⠀⠀⠀⠀
- Bake 18-22mins, or until a toothpick comes out clean⠀⠀⠀⠀⠀⠀⠀⠀⠀
- Cool in tin for about 5 minutes, then remove muffins and place on a wire rack to finish cooling
- Store cooled muffins in an air-tight container*
Jennifer says
Just made this recipe as a fun treat for my kiddo; THESE are muffins!!! Fluffy, moist, and delectable!
Meredith says
I’m so happy to hear you loved these Jennifer! Thanks for giving our recipe a try.
Adelle White says
Question- am i supposed to peel the zucchini first? Thank you!
Meredith says
No need to peel the zucchini!
Courtney Govier says
My kids devoured these. Love all the hidden goodies! They were super tasty!
Meredith says
So glad to hear the kiddos loved these! Thanks for giving the recipe a try Courtney
Marge says
Great use of my garden zucchinis! Will definitely make these again.
Meredith says
I’m so happy to hear you love these muffins too!
David says
I made these a few weeks back with the intention of sharing them with neighbors we haven’t been able to connect with during Covid……….the neighbors didn’t get any…sooo good.
ourlovelanguageisfood says
I’m so glad that you enjoyed them! And your intentions were pure…I’m sure you’ll share with your neighbors when it’s safe to do so!