Chocolate Zucchini Muffins

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The other day, my in-laws gave us a bunch of zucchini from their neighbor’s garden.  I have been wanting to make some chocolate zucchini muffins for a while.  So I set out to make some muffins.  My chocolate zucchini muffins are not only vegan, but they are gluten free as well.  If you like muffins, you may also like my Banana Blueberry Muffins or my Pumpkin Chocolate Chip Muffins.

Chocolate Zucchini Muffins - My Whole Food Life

These muffins not only pack a hidden serving of veggies for the kids, but they are also oil free as well.  This recipe is very easy to make and freezes well too.

Chocolate Zucchini Muffins

Chocolate Zucchini Muffins

Rating: 51

Prep Time: 10 minutes

Cook Time: 10 minutes

Total Time: 20 minutes

Yield: 12 stanard sized muffins

Chocolate Zucchini Muffins

A healthier muffin with a hidden serving of veggies!



  • Preheat oven to 350.
  • Mix all the dry ingredients in one bowl.
  • Mix wet in another bowl.
  • Add wet to dry and mix until combined.
  • Fold in the chocolate chips.
  • Spoon batter into lined or greased muffin pans. I use silicone liners that work awesome.
  • Bake for 15-17 minutes, or until a toothpick comes out clean.

*** If you use a medium to large sized zucchini, you will need to squeeze out the excess moisture.

80 thoughts on “Chocolate Zucchini Muffins

  1. Oh wow….these will be POPULAR in my house! We aren’t gluten free….could I just sub regular flour or whole wheat flour for the gf oat flour? Or is it more complicated?

      1. I just made these muffins and they were very dry and dense. I used 2 eggs and all purpose g.f. Flour. However, my zucchini had been frozen. I let it thaw out then drained it thinking it would make the batter too moist. I was very wrong. They didn’t
        Rise much either. Any suggestions, because I would really like to perfect this recipe and use again.

        1. I am not sure what happened. A lot of people actually say the recipe comes out the opposite way. Maybe it was because of the frozen zucchini? I’m sorry it didn’t work out for you. :(

        2. The reason why they were dry is because zucchini baked good recipes need the moisture from the zucchini to get that moist texture. Next time, I would try leaving the liquid in the frozen zucchini instead of draining it.

  2. Do you think I could sub coconut oil for the applesauce? I’m out of applesauce and I want to make these in the morning.

  3. My toddler and I made these together this afternoon. Messy but fun and delicious! Might try whole wheat flour next time since he prefer a less moist, denser texture. Wish we could make these into crunchy cookies! I am sure they will be a hit at play group tomorrow, thanks!

  4. Just in case anyone is wondering, I entered the ingredients on for nutrition info. Per muffin it’s only 124 calories, 21g carbs, 4g fat, 4g protein, 123g sodium, and 9g sugar. It didn’t list fiber but I calculated out with the zucchini, oat flour, flax, and applesauce it is almost 2g fiber per muffin.

  5. When you say oat flour – does that mean I can put quaker oats in my food processor and grind it up to make oat flour? Or is it something different?

  6. I love the idea, but the photo makes them look like they have a very dense, “packed” structure. This is perhaps because of the lack of gluten? How does one get around that, then?

    1. I don’t think they were dense at all. In fact, I think if you used whole wheat flour, they would be more dense.

  7. I think this recipe is AMAZING!!! Can’t wait to try it!!! Thank you VERY much for sharing!!! :)
    Do you think I could use honey instead of maple syrup?

  8. Can i use 2 regular eggs instead of the flax eggs? I just made pumpkin muffins with oat flour and they were so moist and delicious! I cant wait to try these!

  9. Also, any chance yellow squash could be used in this recipe? They are interchangeable in so many recipes but wasnt sure about breads/muffins

  10. I made these yesterday and they are delicious. My 10yr old son loves them too. Could you use cacao instead of cocoa? If so would the quantity be the same.

    1. Thank you! Glad you liked them. You could use cacao, but it will be slightly more bitter in taste. I would use a little less too.

  11. Used whole wheat flour and the batter seemed a bit dry so added 1/4 cup of Greek yogurt. VERY VERY tasty, a bit dense but yummy and chocolaty!

  12. I’m just sorry it took me this long to make these delicious muffins! We’ve been buying a similar muffin from Costco, and I’m so happy to replace that expensive treat with a homemade version. These were fantastic and I hate to say it, but the first round didn’t last ten minutes in my house. I’m going to have to find a way to pace ourselves! Thanks for sharing!

  13. I just made this recipe and it is fabulous! Put the mix into a loaf tin and cooked for 40 mins. Delicious! Thank you so much Melissa!!

  14. Hi Melissa, I am going to try these today. Do you peel the zuchinni? And in your opinion what is best way to shred them? Sorry for silly questions but new to all this! :-)

  15. made these the other day. delish! I subbed coconut oil for applesauce for lack of applesauce. they were rich and delicious. dense and chocolatey. Really terrific. They took MUCH longer than 12-14 minutes to bake though, fwiw. More like 20-25. Will def make again. I’ll add shredded coconut for texture next time, to make them even more substantial. Thank you!!

    1. I had the same issue with baking time. I baked mine for 27 minutes, but when I broke one open it was still gooey inside. I’ve made a couple of Melissa’s other muffin recipes with no issue, so I’m pretty confident it’s not an oven calibration issue. I did sub white whole wheat flour for the oat flour, maybe that was it? They also stuck BAD to the paper liners. Will try again! :)

      1. I used silicone liners, so I didn’t have a problem with them sticking. I wonder why they would stick to the paper ones? Can you try and bake yours longer? Also, I think it depends on the size of the zucchini. The smaller ones, which I used, do not release as much liquid.

        1. I had the same issue with the paper liners. The part that cooked stuck to the liner and would not come out and the rest was still raw after baking for an hour. I bought the silicone pan and will try again. Any idea as to why that happened? I like the idea of putting it in a loaf pan as well.

          1. Did you use a larger zucchini? If so, they tend to release more moisture. I used a small one and had no issues. If you use a larger zucchini in the future, you can squeeze out the excess moisture before using it in this recipe. As for the paper liners, maybe you can spray or brush them with oil prior to using?

      1. Sorry you had an issue with them. Did you use a larger zucchini? They hold more water. I mention that in the instructions.

  16. These were delicious! I don’t think I cooked mine long enough as they were slightly moist in the middle but I didn’t mind :-) fudgy goodness!

  17. I’m making these at the moment and I had to put them in the oven way longer then listed. I tried one muffin after 17min and it was really gooey so I put it back in the oven for an additional 10 minutes and the toothpick was still not coming out clean so there’s still in there… what did I do wrong!? I followed the instructions perfect :(

    1. Did you use a larger zucchini? If so, they tend to hold more moisture. I used a small zucchini for mine. Can you just cook them longer?

  18. Just made these muffins this morning & they are delicious! They were very light & fluffy & I wondered if you had a suggestion on how to make them a denser/heavier cupcake?

  19. They are delicious! I can’t stop making them and S.O. won’t stop eating them. Used less maple syrup and added fresh cherries!
    Thank you for posting all these recipes! Your FB posts are one of the highlights of my day!

  20. Melissa,
    These muffins, as you sometimes say are “The bomb” Lol! For all you folks that are finding these muffins “to dense” or “not cooked in the center” or “sticking to the liners” Follow The Directions!!!!! The recipe is written the way it’s written for a reason. Hahaa… It cracks me up to hear people say that they didn’t come out right when they didn’t follow directions. It says to bake these for 15-17 min OR until a toothpick comes out clean, which usually indicates that it could take a bit longer:) Duh! Everyones oven is different. Also to squeeze any excess water out of the zucchini. This is Huge! I noticed nobody replied to Melissa when she asked if they used a bigger zucchini. Perhaps that could very well have been the problem??? Silicone liners work AWESOME! Just sayin :) Thanks Melissa, your the bomb hunny!

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    1. Coconut flour can be fickle to bake with. It’s not an equal sub. You also usually need to add a lot of eggs to help with the binding.

  22. Delicious!!! Just made these for back to school treats and I’m not sure there’ll be any left tomorrow. Love that they are freezer friendly too. Thank you!!

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