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These Healthier Chocolate Chip Zucchini Muffins are made with real food ingredients for a lighter treat but with all the flavor, texture, and delicious you expect in a zucchini muffin. Truly a gluten-free and dairy-free snack you can’t resist! Enjoy them post workout, or for breakfast or a low-calorie snack!

A stack of three chocolate chip zucchini muffins on the table with more in the background and chocolate chips on the table and the top muffin is missing a bite.
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Who’s ready to enjoy a healthier chocolate chip zucchini muffin? There’s nothing better than a chocolate chip zucchini muffin, unless it’s made better for you!

These are made with whole food ingredients. No fake sugar additives or processed ingredients are involved — just real food. Yes! Treats can be made with real food and these are some darn real food treats!

If you love these healthy zucchini muffins you’ve got to try these banana oat muffins or butternut squash muffins.

Why You Will Love This Healthy Zucchini Muffins Recipe

  • Simple, yet healthy ingredients. There’s nothing out of the ordinary needed to make these best zucchini muffins — just a handful of pantry staples and fresh zucchini.
  • Easy to make. These muffins take just minutes to make and just one bowl to dirty up so cleanup is a snap too!
  • All occasion treat. These zucchini muffins with chocolate chips work great any time of day but also to serve for a family brunch or special occasion lunch.

Ingredients

Ingredients to make healthy zucchini muffins on the table in bowls before mixing together.
  • Zucchini: Use fresh zucchini and shred it for the recipe. I shredded mine by pulsing in a food processor but you can easily do it with a handheld grater. I did not squeeze out the liquid in my zucchini beforehand. I found I did not have to.
  • Egg Whites: Using egg whites instead of whole eggs reduces the fat and cholesterol for a healthy zucchini muffin. You can use two whole eggs if you prefer. Make sure they are at room temperature before mixing together.
  • Milk: I am using unsweetened almond milk but you can swap it for another non-dairy milk or even use regular dairy milk if you prefer. It’s important to use unsweetened and unflavored so you don’t add more sugar or any flavorings that may interfere with the flavor.
  • Maple syrup: A less processed sugar for sweetening the muffins. You can use a zero calorie syrup if you like or honey instead.
  • Oil: Adds moisture to the muffins. You can use extra virgin olive oil or melted coconut oil depending on your preferences. Some coconut oils have a bit of flavor which may be slightly noticeable in the muffins but it works unless you don’t like coconut.
  • Vanilla extract
  • Oat Flour: Make sure you oat flour or oats are gluten-free if you need them to be. While oats naturally don’t contain wheat they are often processed in facilities with wheat so there may be some cross-contamination. If you can’t find oat flour you can also make your own with regular old-fashioned oats.
  • Cinnamon and salt: Cinnamon adds warmth and natural sweetness simply making the muffins taste better while salt brings everything together.
  • Leavening: These zucchini muffins use a combination of baking powder and baking soda to cook up light and fluffy.
  • Mini dairy-free chocolate chips: I highly recommend the mini ones because they work much better in the muffins than the regular-sized chocolate chips. Feel free to use regular semi-sweet chocolate chips if you don’t need them dairy-free.

Variations & Dietary Modifications

  • Skip the Chocolate Chips: You can easily leave the chocolate chips out for plain zucchini muffins!
  • Add Nuts: Pecans, pistachios, and walnuts all work great chopped up and added to the batter at the same time as the chocolate chips.
  • Different Flavored Chips: Try these with dairy-free white chocolate chips or even dark chocolate if you like a more intense chocolate flavor.
  • Berries: Swap the chocolate chips for small blueberries or raspberries!

How to Make Chocolate Chip Zucchini Muffins

Preheat oven to 400 F. Prepare a muffin pan with nonstick spray or line with muffin liners. 

Mixing the liquid ingredients in a mixing bowl with a wooden spoon.

Step 1: Combine the eggs, maple syrup, milk, vanilla extract and extra virgin olive oil in a mixing bowl and stir until smooth.

Shredded zucchini is added to the bowl of liquid ingredients and a wooden spoon is leaning on the side of the bowl in the batter.

Step 2: Add the shredded zucchini and stir into the mixture.

Flour is added to a bowl with visbile piles of cinnamon and other dry ingredients on top.

Step 3: Combine the flour, cinnamon, baking powder, baking soda and salt in another bowl and whisk together.

Dry ingredients are added to the bowl of wet ingredients with a wooden spoon in the bowl.

Step 4: Add the dry ingredients to the wet ingredients in small amounts.

Zucchini muffin batter in a bowl with a wooden spoon to the side.

Step 5: Stir together to incorporate the into the batter.

Chocolate chips are visible on top of the zucchini muffin batter.

Step 6: Add the chocolate chips and stir into the batter.

Chocolate chip zucchini muffin batter poured into a muffin tin and chocolate chips on top.

Step 7: Spoon the batter into the 12 muffin cavities. Be sure it’s divided evenly among each cavity. 

Chocolate chip zucchini muffins after baking and still in the baking pan.

Step 8: Bake the muffins at 400 F for 17-20 minutes or until a toothpick can be inserted clean in the muffins. Cool the muffins in the pan 10 minutes before removing them and cooling on a baking rack.

Serving Suggestions

Whether on their own or added to a meal, these zucchini chocolate chip muffins are always a hit! Here are a few ideas for a bit of inspiration.

They are ideal for a quick breakfast in the morning or one on the go! Add a chocolate fudge protein smoothie, slice of berry yogurt bake, or a protein smoothie bowl for a more balanced meal.

Serve them up with your favorite egg dishes for breakfast at home or a weekend brunch. I love them with this veggie egg bake and my salsa egg muffins.

Chocolate chip zucchini muffins on a piece of parchment on the table with a bowl of chocolate chips and more scattered around the muffins on the table.

Expert Tips

  • Store: Store leftover muffins in an airtight container in the refrigerator up to 7 days or you can freeze them for up to three months if you need longer storage. Thaw them out on the counter when you’re ready to serve them.
  • Cool before storing: Allow the chocolate chip zucchini muffins to cool completely before storing them to prevent moisture from building up in the container.
  • Don’t mix too much. You want to just mix until the ingredients come together. Mixing the dough too much may lead to tough muffins.

Recipe FAQs

How do I make my own gluten-free oat flour?

It’s quite easy to do. Place regular oats in a blender or food processor and blend until the mixture is broken down to a texture similar to flour. Make sure your oats are gluten-free so your flour is also gluten-free.

How do I know my zucchini breakfast muffins are done?

Ovens don’t always cook in the same amount of time so I recommend checking them a little earlier than the time in the recipe card. The muffins are done when you insert a toothpick into the center of the innermost muffins and the toothpick comes out mostly clean. You want a few clinging pieces of muffin but not wet dough.

Can I make mini muffins?

Sure! You can easily make these into mini muffins. I suggest checking the muffins after 10 minutes as they will likely cook in less time than full-sized muffins.

Healthy zucchini muffins laid out on a piece of parchment with a bowl of zucchini noodles in the background.

More Healthy Muffin Recipes

If you tried this zucchini chocolate chip muffins recipe or any other recipe on my website, please please leave a 🌟 star rating and let me know how you go in the 📝 comments below.

Chocolate chip zucchini muffins on a piece of parchment with one missing a bite, out of the paper and turned to show bite facing up.
5 from 3 votes
Servings: 12 muffins

Healthy Zucchini Chocolate Chip Muffins

These healthier Chocolate Chip Zucchini Muffins are made with real food ingredients for a lighter treat but with all the flavor, texture, and delicious you expect in a zucchini muffin. Truly a gluten-free and dairy-free snack you can't resist! Enjoy them post workout, or for breakfast or a low-calorie snack!
Prep: 10 minutes
Cook: 20 minutes
15 minutes
Total: 45 minutes
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Ingredients 

Instructions 

  • Preheat oven to 400 F. Prepare a muffin pan with nonstick spray or line with muffin liners. 
  • In a large mixing bowl, combine the eggs, maple syrup, milk, vanilla extract and extra virgin olive oil until smooth. Add the shredded zucchini and stir into the mixture.
  • In a separate bowl, combine the flour, cinnamon, baking powder, baking soda and salt. Slowly fold the dry ingredients into the wet ingredients and stir to incorporate. Last, stir in the chocolate chips.
  • Spoon the batter into the 12 muffin cavities, dividing it evenly among each cavity. 
  • Bake at 400 F for 17-20 minutes or until a toothpick can be inserted clean in the muffins. 
  • Cool the muffins in the pan 10 minutes before removing and placing on a wire baking rack to cool completely. Store in the refrigerator up to 7 days. 

Notes

  • *I have not tested other flours with this recipe. Almond flour will likely work, but you may need a little less as it is a bit more dense than oat flour. You can use oats to make oat flour if you want to. Your flour does not need to be gluten free unless you are gluten free.
  • If you are dairy-free, ensure you are using dairy-free milk and chocolate chips. If you are not dairy-free, you can use regular ones.
  • You can swap the egg whites for 2 whole eggs. Note, the calories will be higher, dietary fat higher and protein will be lower with that swap.
  • Store leftover muffins in an airtight container in the refrigerator up to 7 days or you can freeze them for up to three months if you need longer storage. Thaw them out on the counter when you’re ready to serve them.
  • Allow the chocolate chip zucchini muffins to cool completely before storing them to prevent moisture from building up in the container.
  • Don’t mix too much. You want to just mix until the ingredients come together. Mixing the dough too much may lead to tough muffins.

Nutrition

Serving: 1muffin, Calories: 188kcal, Carbohydrates: 21g, Protein: 4g, Fat: 10g, Saturated Fat: 2g, Polyunsaturated Fat: 1g, Monounsaturated Fat: 6g, Trans Fat: 0.004g, Cholesterol: 0.3mg, Sodium: 136mg, Potassium: 193mg, Fiber: 2g, Sugar: 8g, Vitamin A: 24IU, Vitamin C: 2mg, Calcium: 58mg, Iron: 1mg

Nutrition information is automatically calculated, so should only be used as an approximation.

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Megan

Megan is a nutritionist who coaches women 35+ lose weight sustainably. She is the author of the Low Calorie Cookbook, fitness instructor, host of the Dish On Ditching Diets Podcast and creator of Skinny Fitalicious where you get lighter, higher protein recipes. Follow Megan on Facebook, Pinterest, YouTube and Instagram for the latest updates.

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34 Comments

  1. Sarah Kavanagh says:

    These muffins are awesome! Moist and not too sweet! On the regular rotation now!!!

  2. Kirstin says:

    Can you use honey instead of maple syrup?

    1. Megan says:

      Yes, this was mentioned in the blog post under the ingredients.

  3. Angela Drake says:

    Could I use 3 whole eggs rather than 4 whites? I know it will have more Calories but those 4 egg yolks will be wasted otherwise. Tried freezing them. Ick.

    1. Megan says:

      You could use 2 whole eggs instead of 4 egg whites. You could also use liquid egg whites if you do not want to waste the yolks. With the swap, the calories will not only increase, but the protein will decrease and I’m not sure how the higher fat content from the two eggs will impact the baking results.

  4. Michelle says:

    I’m not sure why mine came out so oily. I used melted coconut oil in place of the olive oil.
    Did anyone else have this problem?

    1. Megan says:

      Mine don’t turn out that way when I use olive oil. Coconut oil is denser than olive oil so it makes sense that they would be oily because there would be too much moisture.

  5. Miz Helen says:

    Your Muffins look awesome. Hope you are having a great day and thanks so much for sharing with Full Plate Thursday.
    Come Back Soon!
    Miz Helen

  6. GiGi Eats says:

    These muffins wanna get in my facee!

    1. Megan says:

      I will gladly put one in your face. 😉

  7. Laura @ Sprint 2 the Table says:

    Oy… I am so sorry you can’t catch a break! Things will settle down eventually. During hard times I always like to remember that it can always get worse. Sounds depressing, but it’s true. Or maybe I’m a hopeless pessimist…

    1. Megan says:

      That to me sounds more like an optimist.

  8. Becca @ The Earthlings Handbook says:

    Wow, too many problems at once! I am sending you healing thoughts. Making muffins for yourself is a great idea–you deserve them, and maybe you also can use them as a bargaining tool to encourage friends to help you so you can get more rest.

    1. Megan says:

      Thank you Becca. I really appreciate your kind words.