These healthy and vegan carrot zucchini muffins are easy to make in one bowl and a great way to use extra zucchini.

Two carrot zucchini muffins stacked on one another. The muffin on top has a bite out of it so you can see the texture and bits of grated carrot and zucchini inside.


These delicious vegan carrot zucchini muffins make a tasty and healthy snack to enjoy any time of day. Packed with flavour and nutrition, they’re the perfect for breakfast muffins, lunch time or an evening treat.

Using zucchini adds extra moisture for a tender muffin and both carrot and zucchini pair well with the cinnamon, nutmeg and coconut sugar.

The recipe is also made with whole wheat flour for extra fiber and features additional nutritious ingredients like applesauce and flax.

Moist, fluffy and bursting with flavour, these are always a huge hit with the whole family.

New to adding to zucchini to sweet recipes? You’ll also have to try Vegan Zucchini Bread, Healthy Zucchini Brownies and Zucchini Chocolate Chip Cookies.

For more carrot treats, this Carrot Cake Banana Bread, Carrot Oatmeal Cookies and Carrot Cake Baked Oatmeal are all great too.

Ingredient Notes

All the ingredients for making carrot zucchini muffins gathered in various small dishes. Each ingredient is labelled with text overlay.
  • Zucchini: You’ll need one medium-sized zucchini or about 1 heaping cup after you squeeze out the liquid. The amount doesn’t have to be exact.
  • Carrot: Use about 1 cup of peeled and finely grated fresh carrot. It’s fine to omit either the carrot or zucchini if you only have one available.
  • Coconut Sugar: Use coconut sugar for a refined sugar-free recipe or you can substitute brown sugar.
  • Maple Syrup: Use any variety of maple syrup or substitute agave syrup.
  • Coconut Oil: This may be substituted with plant-based butter.
  • Flax: You’ll need ground flax seeds (flax meal) to act as a flax egg and help bind the recipe. Do not use whole flax seeds.
  • Almond Milk: You can use any plant-based milk you enjoy here such as oat milk, soy milk or cashew milk. Unsweetened milk is recommended but you can use sweetened milk if you like.
  • Flour: The recipe calls for whole wheat pastry flour. You can substitute white whole wheat flour or all purpose flour. I would not recommend regular whole wheat flour for this recipe.

The complete list of ingredients with measurements is found in the recipe card at the end of the post.

Variations & Additions

  • Chocolate Chips: Fold up to 1/2 cups chocolate chips, mini chocolate or dark chocolate chips into the batter before baking.
  • Mini Muffins: To make mini muffins, use a 24-piece mini muffin pan and bake for 15 before checking for doneness.
  • Extras: You can add in 1/2 cup of extras such as dried cranberries, raisins, chopped dates, walnuts or pecans.
  • Cream Cheese Frosting: For a treat, make the cashew cream cheese or cream cheese frosting from this vegan carrot cake recipe and frost your muffins.
  • Oats: Add 1/2 cup rolled oats to the batter with the dry ingredients or try adding zucchini or carrot to these Healthy Oatmeal Muffins.

Step-by-Step Instructions

Step 1: Prepare for Baking

Hand squeezing grated zucchini over a strainer to remove excess water.

Preheat the oven to 350˚F (180˚C) and line a muffin pan with 12 paper liners. Spray the liners with non-stick cooking spray (not required but makes sure they won’t stick).

Grate the carrot and zucchini then squeeze the shredded zucchini over a strainer to squeeze out excess moisture. Don’t skip this step or the muffins will be soggy and dense.

Peel and grate the carrot as well.

Step 2: Mix Wet Ingredients

Raw carrot zucchini muffin batter in a mixing bowl with a wooden spoon.

Add the zucchini, carrot, applesauce, coconut sugar, maple syrup, coconut oil, flax and milk to a mixing bowl and mix until well combined.

Step 3: Add Dry Ingredients

Raw carrot and zucchini muffin batter mixed in a mixing bowl with a wooden spoon in it.

Add the flour, baking powder, baking soda, spices and salt and mix gently until all the flour is incorporated, then stop mixing.

Step 4: Bake Muffins

12 baked carrot zucchini muffins in a muffin pan.

Divide the muffin batter between the 12 muffin liners by adding one heaping spoon to each then dividing the remaining batter between them.

Bake the muffins for 18-20 minutes or until a toothpick inserted into the center of a muffin comes out clean.

Step 5: Cool and Enjoy

Let the muffins sit in the pan for at least 5 minutes before transfer to a wire rack to cool completely.

A small carrot zucchini muffin sitting on the edge of a baking rack with more muffins in the background..

Recipe FAQs

Are carrot zucchini muffins healthy?

Carrot zucchini muffins can be a healthy choice depending on the specific recipe and ingredients used.

This recipe is a source of fibre, vitamins and minerals. It uses whole wheat flour to increase the fibre content, applesauce to add more nutrition and reduce added oils and fats, and coconut sugar and maple syrup for a refined sugar-free recipe.

Of course, they’re still muffins but can certainly be enjoyed in moderation and as part of a balanced diet.

Can I freeze carrot zucchini muffins?

Yes, you can freeze carrot zucchini muffins. To freeze them, let them cool completely to room temperature.

Once cooled, wrap them individually (not required) then store in a freeze bag, removing as much air as possible before sealing to help prevent freezer burn. Freeze for up to 3 months.

To thaw, set them sit at room temperature for 1-2 hours then enjoy as is or lightly warmed in the microwave.

How should I store carrot zucchini muffins?

Make sure the muffins are completely cool before storing. Store muffins in an airtight container at room temperature for 2-3 days or in the fridge for 1 week.

Can I make these muffins gluten-free?

I haven’t tested these muffins with gluten-free flour so I can’t guarantee success. For gluten-free muffin recipes, try my Vegan Buckwheat Muffins or Chickpea Flour Muffins.

Baking Tips

  1. Measuring Accurately: For best results, I recommend using a digital kitchen scale to accurately measure the ingredients.
  2. Over Mixing: Avoid over mixing or the muffins will be dense and gummy. As soon as the flour is incorporated, stop mixing.
  3. Baking: Make sure the oven is fully preheated, get the muffins into the oven right after you fill the cups and do not open the oven until you’re ready to check for doneness at 18-20 minutes.
  4. Flax: Try to use freshly ground or flax that’s been ground within 1-2 months and stored in the fridge. Flax that’s past its best before date may not act the way we need it to in baking (as an egg).
  5. Draining Zucchini: Don’t skip squeezing the liquid out of the zucchini or the muffins will be soggy and dense.
A carrot zucchini muffin cut in half and spread with butter on a plate.

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Two carrot zucchini muffins stacked on one another. The muffin on top has a bite out of it so you can see the texture and bits of grated carrot and zucchini inside.

Vegan Carrot Zucchini Muffins

5 Stars 4 Stars 3 Stars 2 Stars 1 Star 5 from 1 review
  • Author: Deryn Macey
  • Prep Time: 15 mins
  • Cook Time: 20 mins
  • Total Time: 35 minutes
  • Yield: 12
  • Category: Snack
  • Cuisine: American
  • Diet: Vegan
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Enjoy the goodness of 2 nutritious veggies in these moist and fluffy, healthy zucchini carrot muffins.


  • 1 heaping cup grated zucchini (125 g), squeezed of excess moisture 
  • 1 cup (95 g) peeled finely shredded carrot 
  • ½ cup (113 g) applesauce
  • ⅓ cup (43 g) coconut sugar 
  • ¼ cup (80 g) maple syrup 
  • ¼ cup (60 g) melted and cooled coconut oil 
  • 2 tbsp (14 g) ground flax seeds
  • ⅓ cup (80 mL) unsweetened almond milk
  • 1 ¾ cup (210 g) whole wheat pastry flour 
  • 1 ½ tsp baking powder
  • ½ tsp baking soda 
  • 1 tsp cinnamon
  • ¼ tsp nutmeg
  • ¼ tsp salt
  • ½ cup chopped walnuts, optional
  • ¼ cup raisins, optional


  1. Prepare: Preheat the oven to 350˚F (180˚C) and line a muffin tin with 12 paper liners. Spray the liners with non-stick cooking spray.
  2. Drain Zucchini: Prepare the grated carrot and zucchini. Squeeze the grated zucchini over a bowl or strainer with your hands to squeeze out the excess liquid. You should have a compressed ball of grated zucchini when it’s ready. 
  3. Mix Wet Ingredients: In a large bowl, mix the drained zucchini, carrot, applesauce, coconut sugar, maple syrup, coconut oil, ground flax and almond milk until well combined.
  4. Add Dry Ingredients: Add the flour, baking powder, baking soda, cinnamon, nutmeg and salt and gently mix until “just combined”. Do not overmix the batter or the muffins will be tough. Gently mix in the walnuts and raisins if using.
  5. Fill Liners and Bake: Spoon batter into the 12 muffin liners and sprinkle a few chopped walnuts on top of each if desired. Bake 18-20 minutes, or until a toothpick inserted into the middle of a muffin comes out clean and the tops are golden brown. Bake times may vary depending on your oven. 
  6. Cool: Remove muffins from the oven when done and let sit for at least 5 minutes in the pan before transferring to a wire rack to finish cooling.
  7. Storing: Store muffins in an air-tight container at room temperature for up to 3 days, in the fridge for up to 1 week, or in the freezer for up to 3 months.


Substitutions: You can substitute all-purpose flour or white whole wheat flour in place of whole wheat pastry flour. I do not recommend whole wheat flour or the muffins will be too dense. You can use brown sugar instead of coconut sugar. You can use plant-based butter instead of coconut oil.

For best results, use a digital scale to measure ingredients.


  • Serving Size: 1
  • Calories: 156
  • Sugar: 10 g
  • Sodium: 122 mg
  • Fat: 5 g
  • Carbohydrates: 25 g
  • Fiber: 3 g
  • Protein: 3 g