These healthy vegan muffins are packed with zucchini, carrot, flax, apple sauce, and oats, yet they taste like a cupcake so your whole family will happily eat them! Bake up a batch today and have a perfect grab-and-go breakfast for the rest of the week!

Healthy vegan muffins made of zucchini and carrots on a cooling rack.

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Eat these healthy vegan muffins for breakfast every morning with no guilt.  Let your kids have seconds and know that they are just getting another serving of veggies!  Make a big batch to take on trips or just keep them in the fridge or freezer for a quick breakfast or snack.

Why you’ll love this recipe

  • These muffins are packed with veggies, flax seeds, apple sauce, and whole oats!
  • It can easily be made gluten-free.
  • They’re simply delicious and even picky eaters love them!

I came up with this recipe in my never-ending quest to find quick and easy, vegan, gluten-free, and nut-free things that my family will eat for breakfast.  (This seems like an impossible task on many days).  

Everyone in my house loves carrot cake and zucchini bread, so I thought that I would just combine my recipes for those two things and make it a little healthier by reducing the sugar a little and adding some oatmeal, flax, and raisins for more fiber.  To my surprise, they came out great, and they’ve become a staple in our house!

A close up of healthy zucchini carrot muffins on a cooling rack.

Ingredients and substitutions

  • Flax Meal – this is mixed with water and used as an egg replacement.  You can swap out any other vegan egg that is equal to 2 eggs.
  • Zucchini – you will need 1 medium zucchini equaling 2 cups when shredded.
  • Carrots– you will need about 1 large carrot equaling 1 cup when shredded.
  • Vegan Sugar – to make the muffins taste good.  You can cut the sugar in half if you want it less sweet or you can swap it out for another sweetener if you choose.  (I find that I need 1 cup of sugar in this recipe to make my husband and kids happily eat them.) Use organic sugar to be sure it’s vegan.
  • Oil – to make them moist.  You can use any neutral flavored oil that you like or you can swap the oil out with an additional 1/2 cup of apple sauce.
  • Apple Sauce – to provide moisture and help them bind together.  You can swap this out for mashed banana instead if you wish.
  • Vanilla Extract – for flavor.
  • Flour – I have made these with just about every type of flour and it has come out well every time.  You can use regular wheat flour, whole wheat flour, or any grain-based gluten-free flour.  (I don’t recommend almond flour or other grain-free flour).
  • Oats – to add more nutrition and texture to the muffins. I use whole oats, but you can use quick oats or gluten-free oats if needed.
  • Baking Soda – to help the muffins rise.
  • Cinnamon – for flavor.  You can also use pumpkin pie spice for a nice flavor.
  • Salt – for flavor.

How to make healthy vegan muffins

A full printable version of this recipe with ingredient measurements is available at the bottom of this post.

  • Preheat the oven to 350°F (177°C).
  • Mix 1/3 cup flax and 1/2 cup water together and set aside. (This is your egg replacer.)
  • Wash the zucchini, cut off the stem and hard spot on the end, then put into a food processor and chop until fine (or shred with a cheese grater if you don’t have a food processor).
  • Wash and peel carrots then chop fine in a food processor or shred with a cheese grater.
  • Combine the 2 cups of zucchini, and 1 cup of carrots in a bowl, then sprinkle with sugar (this will make the zucchini and carrots release some of their liquid.)
  • Add the flax mixture, 1/2 cup oil, 1/2 cup apple sauce, and 1 tbsp vanilla extract, and stir well.
  • Add the remaining dry ingredients (2 1/4 cup flour, 1 cup oats, 1 1/2 tsp baking soda, 1 tsp salt, 1 tsp cinnamon) and stir until all of the flour is incorporated.
  • Sprinkle in 1/2 cup of raisins, chocolate chips, or nuts if desired.
  • Pour into oiled muffin tins and bake at 350°F (177°C) for 25 minutes until a toothpick inserted in the middle comes out clean.
A collage of 4 pictures showing the process steps for mixing the dry ingredients with the wet and baking the zucchini carrot muffins.

Muffin tins

I like to use mini muffin tins for the kids.  It makes the perfect size for little snacks!  Since my husband also likes to grab one to eat in the car on his way to work, so I make 1/2 of the batch into regular-sized muffins and 1/2 into mini ones.  The mini muffins cook a little faster, so be sure to keep an eye on them and only cook them for about 22 minutes instead of the full 25 minutes.

Gluten-free instructions

These muffins can be made with regular white flour, whole wheat flour, or gluten-free flour.  They come out well with most types.  I have found that when I use the gluten-free flour mixes, my muffins and cakes come out better with the mixes that don’t have sorghum flour in them.  The mixes with sorghum work great for cookies and bread, but for some reason, when I use these mixes with cakes, cupcakes, or muffins, they have a chewy consistency.  The basic rice flour mixes from Trader Joe’s or this one from Betty Crocker work the best for this recipe.

Note: If you are using a gluten-free flour mix that does not contain xanthan gum, add 1 tsp of xanthan gum to the dry ingredients.

Vegan muffins with hidden veggies on a cooling rack.

How to make the muffins healthier

If you are looking for an even healthier muffin, you can replace all of the oil with applesauce and reduce the sugar. 

I have played around with the oil and sugar, and I have found that the proportions that I have listed in the recipe above are the ones that make these muffins taste sweet enough that my kids still love them.  If you want a little extra sweetness or you want to encourage your kids to try them, put a little dollop of frosting on them! 

Storing and freezing

Since these muffins are very moist, I would keep them in the fridge if you are not going to eat them in the first 24 hours.  They will keep well in an air-tight container in the fridge for up to 5 days or in the freezer for up to 3 months.

A top view of zucchini carrot muffins with a dollop of frosting and a blueberry on top.

More breakfast ideas

Zucchini carrot muffin recipe

A close up of healthy vegan muffins with a dollop of frosting and a blueberry on top.
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5 from 9 rating

Healthy Vegan Muffins

Yield: 24 muffins
Prep: 10 minutes
Cook: 25 minutes
Total: 35 minutes
Author: Monica Davis
Zucchini and carrot muffins packed with veggies and fiber from flax and whole oats.
Print Leave a Review Pin Recipe

Ingredients

Egg Replacer:

  • 1/3 cup milled flax seed
  • ½ cup water

Wet Ingredients:

  • 2 cups shredded zucchini
  • 1 cup shredded carrots
  • ½ cup canola oil
  • ½ cup apple sauce
  • 1 tablespoon vanilla

Dry Ingredients:

  • 1 cup sugar , or coconut sugar or Sucanat
  • 2 ¼ cup flour, (If you need it to be gluten-free, I have tested this with most brands of GF flour and they all worked well as long as they were grain-based mixes. I don't recommend grain-free mixes.)
  • 1 cup rolled oats
  • 1 ½ teaspoon baking soda
  • 1 teaspoon salt
  • 1 teaspoon cinnamon
  • 1 teaspoon xanthan gum, ( If you are using gluten-free flour mix without it – Don't add if using regular flour.)
  • ½ cup raisins, (or chocolate chips or nuts)
  • spray oil to coat muffin tins

Instructions
 

  • Preheat oven to 350°F (177°C).
  • Mix 1/3 cup flax and 1/2 cup water together and set aside. (This is your egg replacer.)
  • Wash the zucchini, cut off the stem and hard spot on the end, then put into a food processor and chop until fine (or shred with a cheese grater if you don’t have a food processor).
  • Wash and peel carrots then chop fine in a food processor or shred with a cheese grater.
  • Combine the 2 cups zucchini, 1 cup carrots in a bowl, and sprinkle with sugar (this will make the zucchini and carrots release some of their liquid.)
  • Add the flax mixture, 1/2 cup oil, 1/2 cup apple sauce, and 1 tbsp vanilla extract, and stir well.
  • Add the remaining dry ingredients (2 1/4 cup flour, 1 cup oats, 1 1/2 tsp baking soda, 1 tsp salt, 1 tsp cinnamon) and stir until all of the flour is incorporated.
  • (Sprinkle in 1/2 cup raisins, chocolate chips, or nuts if desired.)
  • Pour into oiled muffin tins and bake at 350°F (177°C) for 25 minutes until a toothpick inserted in the middle comes out clean.
  • Top with a small dollop of vegan buttercream or vegan cream cheese frosting if desired.

Notes

  • Little muffin tins are the perfect size for kids.
  • If using little muffin tins, reduce cooking time by 2-3 minutes.
  • Top these muffins with a little vegan buttercream frosting or use some vegan crumble topping before baking to make it more of a treat!
Serving: 1muffin, Calories: 184kcal, Carbohydrates: 27g, Protein: 3g, Fat: 7g, Saturated Fat: 1g, Sodium: 329mg, Potassium: 161mg, Fiber: 2g, Sugar: 11g, Vitamin A: 930IU, Vitamin C: 4mg, Calcium: 38mg, Iron: 1mg
Did you make this recipe?Please leave a star rating and review below!

*This was originally posted on 6/26/2017.  It was updated on 9/5/20 to include new images and more detailed instructions.

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