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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, 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.
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, including amounts and temperatures, see the recipe card below.
- Prep. Preheat the oven and line a muffin pan with parchment paper liners.
- Whisk the dry ingredients. In a large bowl, whisk together the coconut flour, baking powder, salt, and cinnamon.
- Mix the wet ingredients. In a separate bowl, whisk together honey, eggs, vanilla and almond milk.
- Combine. Add the wet ingredients to the dry ingredients, and whisk or stir just until combined.
- Add the zucchini. Fold in the grated zucchini and chocolate chips. Transfer the batter to the prepared muffin tins. Fill to the top.
- 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.
- 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:
Tools For This Zucchini Muffin Recipe
- Muffin Tin – Featuring a unique corrugated surface design, allowing for even baking and easy release.
- Muffin Liners – Nothing sticks to these!
Healthy Zucchini Muffins
Healthy Zucchini Muffins (Chocolate Chip)
Sneak veggies into your breakfast with this healthy zucchini chocolate chip muffins recipe. They're perfectly moist with melty chocolate!
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Ingredients
Tap underlined ingredients to see where to get them. Please turn Safari reader mode OFF to view ingredients.
Instructions
Tap on the times in the instructions below to start a kitchen timer while you cook.
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Preheat oven to 350 degrees F (177 degrees C) and line a muffin tin with parchment paper liners.
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In a large bowl, whisk together the coconut flour, baking powder, salt and cinnamon.
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In a separate large bowl, whisk together the honey, eggs, vanilla and almond milk.
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Add the wet ingredients to the dry ingredients and whisk just until combined.
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Fold in the shredded zucchini and chocolate chips.
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Transfer the batter to the prepared muffin tins. Fill all the way to the top.
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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.
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Remove from oven and let cool 15 minutes before serving.
Last Step: Leave A Rating!
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Recipe Notes
Serving size: 1 muffin
Nutrition facts are provided as a courtesy. Have questions about calculations or why you got a different result? Please see our nutrition policy.
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54 Comments
Fernanda
0Hi, I’m from Brazil. É a segunda vez que faço essa receita. Eu simplesmente amei! Não precisei adicionar leite de amêndoas e usei stevia, pois em meu país não temos mel zero açúcar. Obrigada por essa deliciosa receita!
“Hi, I’m from Brazil. This is the second time I make this recipe. I simply loved it! I didn’t need to add almond milk and I used stevia, as in my country we don’t have zero sugar honey. Thank you for this delicious recipe!”
Karen
0I’m confused. The recipe above has NO fat (no ghee or butter) listed as an ingredient. Yet people are commenting about it. also— the recipe calls for honey (not erythritol or monk fruit)? I made it with coconut flakes instead of choc chips— it was DELICIOUS but wet. I just made it again with coconut flakes and also tried to dry the zucchini quite a bit. They still look a bit wet— flat– but done. I just took them out of the oven. Comments or suggestions? should I have added fat (besides the coconut milk)? I like the honey.
Wholesome Yum D
0Hi Karen, This recipe was updated July 17, 2023 so some of the comments are about the older version of this recipe. If your muffins were wet, they probably needed to bake for longer, or if you used a different brand of coconut flour that can impact the absorbency. Hope this helps!
Katrina
0Have you ever made this as a loaf instead of muffins? How long do you think to bake that?
Wholesome Yum D
0Hi Katrina, I have not tried that but if you do please let me know the results.
Carol
0Oh my goodness these are a winner! So moist and delicious! The chocolate chips give these a decadent flavor. You think you’re eating something loaded with carbs, but you’re not! Quick and easy to make, which is another added plus. Thank you, Maya, and team for another amazing recipe!
Nancy J
0Absolutely love these muffins. My family and friends agree too. Just the right amount of sweetness and so easy to make. I found they stuck to the paper liners so I spray PAM in the muffin pan instead and they pop right out.
Melanie Sisco
0Can monkfruit be used instead of Erythritol? And can a different flour be used?
Wholesome Yum D
0Hi Melanie, To use monk fruit, I suggest using my Keto Sweetener Guide to get the correct amount. I do not suggest using another flour. Not all keto flours translate the same in recipes.
E
0WOW!! That is The Best muffin I ever had- in any version. I don’t like too sweet, so I still reduced a bit of sugar, used dark chocolate chips- 0 sugar,, but I added extra blueberries:))) they look awesome, baked beautifully, YUMYI. DEFINITELY will make them again.
Stella
0Thank you for such a wonderful recipe, they’re absolutely DELICIOUS!!
Nancy
0I have bookmarked this recipe and made it several times. Love that I don’t have to squeeze zucchini. So moist and yummy tasting. The only issue I had the first time I made it was that muffins stuck to the paper liners and I hate wasting these delicious muffins. I just sprayed my pan very well and no more problems.
Jessica
0These are good! I might try them with cinnamon next time instead of choco chips.
Jay Todgham
0Any substitutes for zucchini perhaps more almond flour
Wholesome Yum M
0Hi Jay, This recipe doesn’t call for almond flour, it will not work in this recipe. If you would like to make muffins without zucchini, I suggest following this recipe for blueberry muffins and replace the blueberries with chocolate chips.
Jessica
0I’ve never made any baked goods with zucchini before, but you have so many good recipes that I might have to try these too!
Wholesome Yum M
0Hi Jessica, I think you’ll be pleasantly surprised! Let us know what you think when you make them!
Anka
0What can I replace the erythrol with? Maple syrup, dates? Many thanks
Wholesome Yum M
0Hi Anka, If you are wanting to use a natural sugar instead of the keto sweeteners, then coconut sugar is our best option.
Doreen Williams
0Way too much Ghee. They were very oily and had an oily after taste.
Cristina
0Love this recipe. Muffins came out moist and flavourful. Love that the zucchini didn’t need to be squeezed. My family loves plain zucchini bread so I omitted the chocolate chips and added 1 tsp if cinnamon instead. Will be a regular recipe while the garden is providing so many zucchini! Thank you!
Jessica
01 tsp of cinnamon instead of the choco chips was a great idea! Thanks!
Donna
0I don’t always have the best luck with keto baked goods; they usually turn out so dry and dense. But these muffins were delicious and so moist. Only substitution I made was to use butter instead of ghee because butter was all I had on hand. And I was far too lazy to make a trip to the store to replenish the ghee. I also added just a sprinkle of cinnamon to the batter. These will definitely be made again. Thank you for such a great recipe.
Raquel
0I’ve been looking for a good chocolate chip muffin recipe for my son who is a type 1 diabetic. These were a total hit! Thank you!
Helene
0Could I replace the eggs in this recipe with chia seeds 6tbsp and water do you think?
Wholesome Yum M
0Hi Helene, I have no tested this method with this recipe, but the recipe should still work.
Val
0I love these low carb, high fiber muffins.
I added 1 teas. Pumpkin pie spice because I find the cinnamon to help my blood sugar.
I eat these in the morning with mashed avo
on top. Thank you for this delicious recipe!
Lindsey Willson
0These look amazing. Thank you for including this veggie packed recipe.
Celeste
0I love zucchini recipes. Can’t wait to make this again!
Nab
0Made these but came out too wet.
Wholesome Yum
0Hi Nab, if your zucchini is especially wet that can happen. If that’s the case, pat it lightly with a paper towel first.
Alex
0Hi! My son is on a very strict keto diet and needs a 3:1 ratio of fat to carb + protein.
Do you absolutely need the 6 eggs? Could I lower to 5 and still have a good outcome?
Maya | Wholesome Yum
0Hi Alex, I haven’t tried that specific amount of eggs, but typically in baking recipes reducing wet ingredients will not produce a good outcome. You might be able to reduce the eggs by one and compensate with more fat, but I haven’t done it to say for sure.
Arionne
0I made these but mine came out way too wet. Next time I will definitely pat the zucchinis dry. My kids are waiting with baited breath to try them because they smell so yummy. They are calling them Grinch muffins since the green tint came through.
Christina
0I’m not a fan of coconut, can I sub almond flour for the coconut flour? If so, is it an even conversion? Thanks
Maya | Wholesome Yum
0Hi Christina, You can’t substitute them, they work very differently. If you want muffins with almond flour try these keto blueberry muffins instead and you can swap the blueberries for chocolate chips if you want to.
Kimmora
0Can I use Monk Fruit in the place of the Erythritol?
Maya | Wholesome Yum
0Hi Kimmora, Yes, you can if it’s a monk fruit blend. Check the conversion calculator here.
Jennifer
0I followed the recipe using ghee (made a double batch). Next time I will try coconut oil as the muffins have a strong ghee flavor which I didn’t care for too much. Not very sweet, but nice and moist. I suggest to form the tops smooth since the batter doesn’t really lay well and ends up with rough patches that cook to little crisps.
Maya | Wholesome Yum
0Thank you for the feedback, Jennifer. You can definite taste the flavor of the fat used (ghee, butter or coconut oil), so I recommend choosing the one that you like best.
Carrie Smith
0These were absolutely delicious. I prefer this recipe to any wheat flour recipe I’ve made. I only put chocolate chips in half of the muffins and actually prefer the ones without. I also used grass-fed butter as I was out of ghee. Thank you for a phenomenal recipe!
Maya | Wholesome Yum
0I am so happy that you liked the muffins, Carrie! Please come back again soon!
Sheri Davis
0I used kerry gold instead of ghee and added some nutmeg. Very good recipe!!
Maya | Wholesome Yum
0I am so happy to hear that, Sheri! Have a great day!
jenny
0These were easy to make and delicious!! Keeper!!
Maya | Wholesome Yum
0I am so happy you liked it, Jenny! Thanks for stopping by!
Diana
0Can you use regular butter to make these?
Maya | Wholesome Yum
0Hi Diana, Yes, you can do that.
Linda
0Easy to make. One over size zucchini from the garden and shredded made more than the 2 cups needed, and I have enough for several more batches. I didn’t have ghee, but read online that you can substitute unsalted butter(melted), which I did, and they baked up nicely. Filling the muffin liners with the batter to a nice rounded top worked well because they didn’t rise. I did wait until they cooled ( sorta) and when I broke them apart into 4ths, they held their consistency. They are tasty, and perfect along with my hot drink. I will make these again!
Maya | Wholesome Yum
0I am so glad you liked it, Linda! Thanks for stopping by!
Sandra Williams
0Thankyou so much. I’m new to eating gluten free and all this information is very helpful and very much appreciated.
Maya | Wholesome Yum
0You are welcome, Sandra! Have a great day!
Evelyn LaTorre
0The ingredients weren’t listed!
Maya | Wholesome Yum
0Hi Evelyn, The ingredients are above, right above the instructions on the recipe card.