Gluten-Free Chocolate Chip Zucchini Noodle Muffins

Gluten-Free Chocolate Chip Zucchini Noodle Muffins

Put a spiralized twist on zucchini muffins with these Chocolate Chip Zoodle Muffins, made with gluten-free, wholesome ingredients for a flavor packed breakfast, dessert, or snack! 

Gluten-Free Chocolate Chip Zucchini Noodle Muffins

Whether you enjoy these as a breakfast or snack, drizzled with nut or seed butter, or as a proper dessert, you’re going to love the simply sweet flavors of these Gluten-Free Chocolate Chip Zucchini Noodle Muffins.

Gluten-Free Chocolate Chip Zucchini Noodle Muffins

Using spiralized zucchini is a much easier way to basically shred zucchini – you just spiralize the zucchini in seconds and then finely chop the noodles on a cutting board before adding them to your batter mix. Shredding a zucchini is more time consuming and I always manage to scuff my knuckles!

These save well, freeze well, and reheat well. They’re one of those desserts you not only enjoy eating, but feel great about, because you’re packing in the nutrients from vegetables! And the zucchini adds a nice moistness to these gluten-free treats and the walnuts pack a welcomed crunch in every bite.

Gluten-Free Chocolate Chip Zucchini Noodle Muffins

Amp up the chocolate factor by drizzling these muffins with some extra melted chocolate chips, or stir in a tablespoon or two of cacao powder.

Watch our video to learn how to spiralize a zucchini using the Inspiralizer and subscribe to our YouTube channel to watch more videos:


Nutritional Information & Recipe

Paleo Chocolate Chip Zucchini Noodle Muffins

Prep Time 20 minutes
Cook Time 30 minutes
Total Time 50 minutes


  • 1/2 cup coconut flour
  • ¼ cup almond flour
  • 1 teaspoon baking soda
  • 1 teaspoon baking powder
  • 1/4 teaspoon salt
  • 2 teaspoons cinnamon
  • ½ teaspoon nutmeg
  • 3 eggs
  • 3 tablespoons maple syrup
  • 2 teaspoons vanilla extract
  • 1 tablespoon coconut oil melted and cooled to room temperature
  • 1 ripe banana well mashed
  • 1 medium zucchini Blade D, noodles well trimmed
  • 2 tablespoons almond milk
  • ½ cup walnuts well chopped
  • ¼ cup dairy-free chocolate chips I use Enjoylife


  • Preheat the oven to 350 degrees.
  • ?Insert liners into a muffin tray with 12 muffin cavities.
  • ?In a medium bowl, add in the coconut flour, almond flour, baking soda, salt, cinnamon and nutmeg.
  • ?In another medium bowl, mix the eggs, maple syrup, vanilla extract, almond milk, coconut oil and banana together.
  • ?Add the dry ingredients to the wet and add in the zucchini and stir until the batter is smooth. Fold in the walnuts and chocolate chips and stir.
  • ?Pour the batter into the muffin tins and bake for 30 minutes or until a toothpick comes out clean when you pierce the center of a muffin.
  • ?Pop the muffins out by pulling on the parchment paper tabs.

with love, Ali

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Recipe Rating


  • Looks wonderful-are you using a large muffin tin to bake them or the regular "cupcake" medium size tin?
  • That parchment paper trick? Never tried it but now I'm going to do that every.single.time. What a great tip! These muffins look fantastic. I just love putting chia seeds in my smoothies!
  • You are so sweet, Ali! My dream is to bake with you one day :)
  • I never thought of using my spiralizer for muffins. I think I'd toss in some of those chia seeds in these!
  • I love this!! I don't find it predictable! I really enjoy classic easy recipes with a healthy twist. Ones that taste good are harder to find than you think!
  • Oooh, these sound sooo good! I would use the chia seeds to make some jelly/jam, which I've seen a lot but never tried. Right now, I just throw chia seeds on my breakfast and in soups to get a healthy dose. :)
  • Can't wait to try this!!!!
  • These look amazing! Since I have no gluten issues but am obsessed with my sprializer... what are your thoughts on using 1/2 c of regular flour?
    • I think the coconut flour adds to the flavor of these muffins and the texture, so I wouldn't swap - plus it's lower in glycemic index which is better for you later on in the day! :)
      • What about almond flour? Aside from flavor- are the measurements the same?
  • I love chia seed "pudding" and try to add them to any baked goods for a health-boost!
  • some blueberry chia muffins
  • Those muffins look great definitely plan to make them soon! I love making "Mama Chia"'s a refreshing way to change up regular water!
  • Can't wait to try these! I wonder if I could try using chia seed "eggs" in these!
  • These sound great! I'm excited to use my Spiralizer for other things, like this kind of thing. Grating zucchini is totally a pain in the butt, and it seems like the noodles would give an interesting texture to the muffin.
  • Is watch muffin 279 calories?
    • Each muffin, yes. To reduce the calorie count, leave out the walnuts!
      • Thanks for clarifying. The nutritional facts (which I LOVE that you always include) is a bit misleading in that it says servings: 6.0. That leads one to believe that 6 muffins equate to a 279 calorie serving.
        • Serving size says "1 muffin" - but it "yields" 6 muffins! Hope that clarifies!
  • The muffins great and so yummy! Thanks for sharing this recipe. I plan to give it a try :)
  • I use chia seeds several times a week, in oatmeal, smoothies, and adding them to breakfast muffins I make my hubby each week. I can't wait to try this recipe!
  • I am currently hooked on a pudding I make using unsweetened almond or cashew milk some sf sweetener, Glucomannan and chia seeds. I have a new recipe for gf and lc bread using chia seeds I want to make.
  • Chia pudding!
  • some suggestions to make this an even healthier snack; if you don't eat egg, you can use either ground flax or chia seeds as a replacement (look up ratio of water to flax or chia). And a low glycemic choice instead of maple syrup is coconut nectar.
  • I'm going to try my hand at homemade energy "gels" for my long runs! I've seen some amazing recipes that require chia seeds for the right texture!
  • I would start with this recipe and work my way on to carrot muffins and chia pudding!
  • Yum - these look great! I love to put chia seeds as egg replacers in just about everything - pancakes, muffins, cookies - you name it!
  • How do you get the zucchini to stay in place on the spiralizer after it's cut lengthwise? It keeps falling off no matter how much pressure I apply !
    • You may be slicing too far halfway (more than halfway!)
  • I have not tried chia seeds yet but have seen the pudding recipe many times. I'd definitely want to do that as well as nutriblasts. :) These scrumptious zucchini muffins are on my to do list also. :)
  • Looks yummy, will replace eggs with applesauce. I like to use chia seeds in my smoothies and overnight oats.
  • Muffins look delicious, I will be trying soon. I would use chia seeds in soup, to add some crunch, protein and nutrients.
  • These look SO good. So good in fact, that I'm considering leaving work right now to go home and make them. I'm sure my boss wouldn't mind as long as I bring him some. And I would throw some of those chia seeds in too because I add them to everything :)
  • these look amazing! I can't wait to try them.
  • I love putting chia seeds in overnight oats!
  • These look great! and I love that you are using coconut flour. Do you think this same recipe would work if I were to make it in a loaf pan instead of muffins?
    • Yes, although the bake time would be different!
  • Can't wait to try this recipe. I don't mind predictable if the result is as yummy as they look!!
  • These look delicious!
  • These look yummy. I just recently resurrected my spiralizer from the appliance graveyard when I saw a friend make some zucchini pasta. I tried it and it was yummy. So I look forward to using it more often. Currently I use chia seeds in my green smoothies. I would use them to try chia pudding.
  • I would make chia pudding! But I usually add them to my smoothies :)
  • Hi Ali, these looks awesome!! Do you think it would work to swap out the oil for unsweetened applesauce? Thanks!
  • Chia Pudding! I love Oh She Glows's Almost Instant Chia Pudding.
  • Just got the app, love it! Also check typo mixture=moisture (wink) in the recipe Ins. #3. Also can sugar-free chips be used and also what could be sub. for banana? Trying to cut the sugars down as much as possible. 16g is too high for me. Any help would be appreciated. :)
  • Muffins are the perfect 'non bakers' baked good as they are simple and don't need to be pretty like a cupcake!! This is a great recipe
  • I agree, perfect...they look delicious! Can't wait to try them!! :)
  • Your zucchini recipe looks wonderful. And I would use a bag of chia seeds for my morning smoothies. Love those little seeds!
  • Love the idea of using the spiralizer for zucchini muffins - better than bread because portion control!
  • More healthy spiralized desserts would be super appreciated! Especially with apple & pear. & I love chia pudding! If that could be incorporated into a spiralized dessert it would be so fitting! Just some ideas. I cant wait to try these muffins. I may make the zucchini into spiralized rice instead of leaving as half-moons. Hope it will still bake up well that way!
  • I love making chia seed puddings and adding chia seeds to smoothies
  • I never have baked with zucchinis before but after seeing these muffins, it is something I must try. I definitely am curious to know what the vegetable addition tastes like!
  • I love adding chia seeds to my morning oatmeal, but also use them in smoothies.
  • Gosh, it looks delicious! It's a must try for me! Yum! I'm cooking on youtube and I've just uploaded a recipe for homemade falafels, hope you will check it out! Thank you! :-) Thank you for an awesome recipe!
  • Very yummy. Like the parchment paper trick
  • I cant wait to make these! MMM!
    • My guess is with the rest of the wet ingredients.
  • These look yummy; you've done it again Ali! One question: I need to find something to substitute for the 3 eggs because my husband is allergic and we are vegan's. You've already got bananas on the list, what about applesauce (if so, how much) or part flegg's and part something else? Sure would appreciate a suggestion or two from you, Meaghan or any of your creative followers! Thanks.
    • Marcia again, sorry to be such a pest. This question is about the number of muffins the recipe makes. You show 6 muffins but underneath that, it says 1 muffin. Can you please clarify? Back to the egg replacer: How about using chia seeds? Again, how much liquid to how many chia seeds? Thx
      • I think it's the recipe plugin that this site uses, it's a bit confusing. It makes a batch of 6 and 1 muffin is a serving. As for the egg replacer, I don't want to recommend something without trying it myself first!
      • I only had two eggs so I made one flax seed egg and it worked just fine! Not sure it would work for three eggs, but worth a try!
  • These look amazing, I can't wait to try them this weekend!
  • I wanted to LOVE these, I bought all the ingredients just to make them, but mine came out really horrble. Kinda souffle like and no matter how long I cooked them they kept the raw texture. I guess gluten free isn't for me!
  • I like making chia seed pudding and putting them in oatmeal and yogurt. These muffins look delicious, can't wait to try them.
  • I've seen chia seeds quite a bit in recipes as a substitute, but have never tried it. I'm sure I could find plenty of uses for them
  • Luv your site. Check it daily for inspiration and fun new recipes to try. The videos are great. Pre-ordered your cookbook and patiently waiting for it to find its way to my front porch! Keep up the good work :-)
  • These look so good! I want to try them!
  • These were WONDERFUL. I used almond flour/meal and tripled the amount (was too runny for me). I also used cashew milk (It's what I had). LOVE IT.... thanks!
  • I love using chia seeds in my oatmeal and yogurt, but they are my absolute favorite in my overnight oatmeal with oats, yogurt, chia, flaxseed, kefir and some berries or banana mixed in the next day!
  • Ahh! I've got everything but the maple you recommend anything else as a substitute? Is it needed or can it be made without? Thanks!
  • Allergic to nuts- are these necessary? Any substitutions?
    • They help with the flavor and consistency, but they aren't 100% necessary!
  • I'm going to make these this weekend and will have to do an egg substitute, since I can't have eggs. I think I'll use the flax substitution b/c I think the chia seed sub may make them too soggy. The substitutions are as follows: 2 tbsp. flaxseed meal, 3 tbsp. water, 1/2 tsp baking powder = 1 egg. Or: 1 tbsp. chia seeds, 3 tbsp. water, 1/4 tsp baking powder = 1 egg. In each case, you'll want to combine the ingredients and let them sit for a few minutes to achieve the right "egg-like" consistency. Will let you know how the muffins turn out.
    • Sorry I made a mistake!! It's 1/4 tsp baking powder with the flaxseed meal, and 1/8 tsp baking powder with the chia seeds.
  • These look delicious!! I would add in your title that these muffins are grain-free, not just gluten-free. When I see gluten-free I assume there is GF flour in the recipe (rice, potato, tapioca, etc.). I almost jumped for joy when I saw they are made out of coconut flour...yay!!
  • I made the muffins following the video, which was a bit difficult to follow. Mine don't look exactly like yours, they are taller and the recipe yielded 9 rather than 6 regular muffins. The batter in the video was dry and lumpy (due to omitting 3 eggs); mine was much smoother and did not require almond milk. I even used extra coconut flour. They turned out very nice! I made some notes on a recipe card to help me out next time. Baking is more precise than cooking so the more detail the better. Thank you for this recipe and all the others here on your website. It is a super helpful and much-appreciated resource.
    • So happy that your muffins came out great! This is awesome to hear.
  • I am going to try some substitutions with these. Flaked coconut and dried cranberries in place of chocolate chips (that will be my first experiment). I also want to try adding drained crushed pineapple in the future. Of course, this will require some adjustments with moist ingredients.
    • This all sounds great! It's all about having fun!
  • I'd love to make these but can't eat bananas, could you suggest an alternative or would they still be OK if I just omitted it? Thanks.
    • Try 1/2 cup unsweetened applesauce, that's worked for me in other recipes
  • I made these and a picky two year old loved them!
  • I made these and a picky two year old loved them!
  • Boo! Way too wet and sunk in the middle. Very disappointing.
  • You don't show squeezing the moisture out of the zucchini in the video. How important is that step?
    • Hi Teresa, We have a few general tips to keep in mind to avoid watery zucchini noodles but generally you want to follow these tips if you're going to serve your zoodles in a sauce, not in baking.
  • Trying the recipe this weekend.
    • Hi Rhonda! Let us know how it turns out!
  • Noodle-muffin sounds so innovative.Can't wait to have this.Thanks for sharing.
    • Of course! You're going to love them!