These healthy chocolate zucchini muffins are made with simple ingredients, have no refined sugar and are dairy free. Super moist, fudgy and delicious with chocolate flavor, they will be a hit in your home! An easy and seasonal breakfast, lunch snack, or even dessert that boasts hidden veggies and is homemade in just 40 minutes.

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Zucchini is in season right now and if you need to be baking these healthy chocolate zucchini muffins and a few other delicious pastries like easy pumpkin zucchini muffins or healthy zucchini bread!
Muffins are one of our favorite choices for healthy breakfasts! If it's not these then we are definitely eating up healthy zucchini muffins, protein blueberry muffins, strawberry yogurt muffins or almond flour banana muffins!
Or, if double chocolate is your thing be sure to try this double chocolate baked oatmeal. Who doesn't love chocolate for breakfast?
These healthy chocolate zucchini muffins are the best! They are also a definite crowd pleaser despite the hidden veggies that come with them, hello zucchini!
Why This Recipe Works
- These healthy chocolate zucchini muffins are perfect to get an extra serving of veggies in the picky eaters in your home!
- Made with almond flour and gluten free.
- No butter, these healthy chocolate zucchini muffins are made with coconut oil.
- Naturally sweetened and refined sugar free, these healthy zucchini muffins are sweetened with coconut sugar (maple syrup or honey are also excellent ways to sweeten them.
- Double chocolate from cocoa powder (or sub with cacao powder) and dairy free chocolate chips. Chocolate for breakfast is always a plus for me!
- Whether you have a garden or stocked up at the farmer's market, this recipe is a great way to use up zucchini. Healthy chocolate zucchini muffins are a healthy muffin recipe is worth turning your oven on in the summer!
- Easy to make ahead for a week's worth of healthy treats!
Ingredients You Need for This Recipe:
Here are the ingredients you need to make this recipe. Reference the recipe card at the bottom for exact measurements and the notes below for substitution ideas.
- Almond flour: be sure to use fine almond flour, not almond meal. You may choose to grind up the almond flour even more if you want an even finer texture.
- Gluten free flour: recommend either Bob’s Red Mill gluten free 1-1 baking flour or King Arthur flour gluten free all purpose flour. Both measure at one-for-one compared to all purpose flour and provide a great texture for gluten free muffins. You could also try using oat flour to replace the all purpose flour.
- Grated zucchini: Generally 1 medium zucchini yields 1 to 1.25 cups of shredded zucchini. You may peel the zucchini if you have picky eaters or may leave it on.
- Non-dairy milk: only add if mixture seems too dry once all other ingredients have been added. You could also add in some yogurt or applesauce as an alternative.
How to Make This Recipe
Below are step-by-step instructions for how to cook this recipe. The recipe card at the bottom shows the exact cooking time and temperatures.
- Preheat oven to 350F. Add dry ingredients to a bowl.
- Mix dry ingredients using a whisk and set aside.
- Crack eggs into a small bowl and beat eggs until well beaten.
- Add remaining wet ingredients to egg bowl and gently mix.
- Add wet ingredients to dry and mix until incorporated. Do not over mix.
- Fold grated zucchini into mixture.
- Fold chocolate chips into mixture until just mixed. Add in oat milk if mixture seems dry.
- Use an ice cream scoop to scoop out 12 muffins into silicone liners sprayed with coconut oil spray.
Expert Tips
- Some readers have commented that the batter is too dry. The batter will appear much thicker and dry compared to traditional muffin batter. However, almond flour is a high-moisture flour and they will not bake up dry. If you are so inclined you can add a bit of almond milk to make them a bit easier to stir.
- To avoid texture issues with picky eaters, be sure to grate the zucchini on the smallest blade on the shredder you have. You can also peel the green skin from the zucchini before you shred it to mask even more green.
- Consider grinding the almond flour in a food processor prior to mixing the dry ingredients. This will help the batter to be smoother.
- Do not over-mix. Gently mix and stop once the ingredients are incorporated
- To make healthy chocolate zucchini muffins with no oil you can sub out unsweetened applesauce or mashed banana. Sub in applesauce or mashed banana and making them without oil will result in a lower fat muffin.
- To make these vegan zucchini muffins, swap out the egg for a flax egg or applesauce.
- Store muffins in an airtight container in the refrigerator for up to five days. Reheat in the microwave for 20-30 seconds.
- Muffins may also be frozen and stored in freezer-safe containers for up to 3 months.
- Top healthy chocolate zucchini muffins with a dab of almond or peanut butter and some extra chocolate chips!
FAQs
No, the zucchini in these muffins is so light and lends such perfect moisture to these muffins without a veggie taste.
I recommend refrigerating these muffins in an airtight container for up to 5 days.
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If you've made this recipe, would you please leave a star rating and comment below on the recipe card? If you want more simple + delicious eats, please subscribe to my newsletter and follow along on Facebook, Pinterest, and Instagram for the latest updates.
Healthy Chocolate Zucchini Muffins
Ingredients
Dry Ingredients
- 3 cups almond flour
- ¼ cup gluten-free flour
- ¼ cup cocoa powder or cacao powder
- 1 teaspoon baking soda
- 1 teaspoon ground cinnamon
- ½ teaspoon salt
- ½ cup coconut sugar or maple syrup
Wet Ingredients
- 3 eggs beaten
- ¼ cup unsweetened vanilla almond milk may add more if dough seems dry
- ½ cup coconut oil melted
- 1 teaspoon vanilla extract
Other Ingredients
- 1 cup zucchini shredded
- ⅓ cup Enjoy Life Brand chocolate chips
Instructions
- Preheat oven to 350F. Place 12 muffin liners into muffin pan and spray with cooking spray.
- Combine flour, sugar, baking soda, cocoa powder, cinnamon and salt in a bowl. Use a sifter if you have one.
- Mix egg, coconut oil, almond milk and vanilla extract into a bowl. Stir into dry ingredients until just moistened. Fold in zucchini and chocolate chips.
- Use an ice cream scoop to portion out 12 muffins. Bake for 20-25 minutes or until a toothpick comes out clean.
Notes
- To avoid texture issues with picky eaters, be sure to grate the zucchini on the smallest blade on the shredder you have. You can also peel the green skin from the zucchini before you shred it to mask even more green.
- Consider grinding the almond flour in a food processor prior to mixing the dry ingredients. This will help the batter to be smoother.
- Do not over-mix. Gently mix and stop once the ingredients are incorporated.
- To make these with no oil you can sub out unsweetened applesauce or mashed banana. Sub in applesauce or mashed banana and making them without oil will result in a lower fat muffin.
- To make these vegan zucchini muffins, swap out the egg for a flax egg or applesauce.
- Store muffins in an airtight container in the refrigerator for up to five days. Reheat in the microwave for 20-30 seconds.
- Muffins may also be frozen and stored in freezer-safe containers for up to 3 months.
Karen
I made these last week and they were gone in a couple of days. The kids, the neighbor kids and everyone LOVED these. I used chia seeds (soaked) instead of egg because of my son’s allergy, a tiny extra zucchini because I shredded extra on accident, the maple syrup option and a mix of almond flour and regular flour. They were super moist and delicious! Thank you! We will be making them again for a friend brunch tomorrow.
Lyndsey
Hi Karen! Thank you so much for your kind review. I'm so glad they worked out for you!
CS
Made this recipe tonight and was disappointed... I followed it to a T but they did not have much flavor and tasted awful. No one in my family of four liked them so they ended up in the trash. 🙁
Lyndsey
So sorry they didn't work out for you.
Marie
Made these when my clean-eating family was visiting...everyone gave a thumbs up! Definitely a keeper recipe...made a second batch immediately ❤️
mommafitpgh@gmail.com
I'm so glad your family loved them! Thanks for making them 🙂
Brandi
If I used all gluten free flour, do you know how much I would use?
mommafitpgh@gmail.com
I haven't made this recipe with all gf flour but I would start with one and add as needed until the texture resembles muffin batter. Hope that helps!
Alyssa M
If you don't have coconut sugar can you use another type of sweetener like erythritol?
I can't wait to try this out!
mommafitpgh@gmail.com
you could def try! I like Lakanto one for one monk fruit sweetener when I'm opting for a low carb sweetener.
Terra
Made these over the weekend and they turned out amazing! My mom used to make zucchini bread when I was a kid so this chocolatey version brought back some good memories. And your healthy swaps make it guilt-free! I used coconut flour for the 1/4 cup of gluten-free flour and the texture turned out great. This recipe is a keeper!
mommafitpgh@gmail.com
I'm so glad you liked it! love that you used coconut flour, I'll have to try that 🙂
Aleah
I’m trying this recipe! We don’t have any allergies, so I used regular flour and regular sugar. The dough turned out really dry.. I’m not sure the proportions are right. What is the consistency of the dough supposed to be like before you put it in the oven?
mommafitpgh@gmail.com
it should be like muffin dough, definitely not dry. Did you bake them? wondering how they came out
snl
OMG mine too! I used coconut flour and the required sugar but the dough was soooo dry! I ended up mixing it up with another recipe I found because no way were these muffins going to turn out good. Yikes.
mommafitpgh@gmail.com
coconut flour and almond flour are very different in how they bake. If you used the same amount of coconut flour as almond flour they would definitely be dry. the ratio of coconut to almond flour is 1/4 cup coconut to 1 cup almond flour. Coconut flour is inherently dry so you need very little for baking.
Dawn Conklin
I am lucky that my kids are not quite so picky, tho one of them does sometimes not like something just because it has certain things in them. But chocolate muffins she would try no matter what!
I use the Instant pot a lot. If you cook veggies in with a brown rice in the IP, they will blend right into the dish without being noticed. Brown rice takes longer to cook so the veggies get nice and soft. And you are still keeping the nutrients in - they are more done then you might prefer for taste, but the kids will eat them without knowing 🙂
mommafitpgh@gmail.com
love that idea! and in the IP makes it that much easier. Thanks for the great tip!