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The best recipe for healthy zucchini muffins.

Healthy Zucchini Muffins

5 Stars 4 Stars 3 Stars 2 Stars 1 Star 5 from 4 reviews
  • Author: Erin Jensen
  • Prep Time: 20 minutes
  • Cook Time: 32 minutes
  • Total Time: 52 minutes
  • Yield: 12 muffins 1x
  • Category: Dessert
  • Method: Oven
  • Cuisine: American


Healthy Zucchini Muffins Recipe – you are going to love how fluffy these healthy zucchini muffins are! So easy and delicious!



Dry Ingredients:

  • 1 cup 1-to-1 gluten-free flour
  • 1/2 cup almond flour
  • 1/2 cup gluten free oats
  • 1 tablespoon tapioca starch
  • 1 1/2 teaspoons baking powder
  • 1 1/2 teaspoons baking soda
  • 1 teaspoon cinnamon
  • 2/3 cup coconut sugar
  • 1/8 teaspoon xanthum gum
  • 1/8 teaspoon kosher salt

Wet Ingredients:

  • heaping 1/2 cup unsweetened applesauce
  • 1/4 cup banana, smashed (about 1 small banana)
  • 1/2 cup unsweetened almond milk
  • 2 flax eggs
    • 2 tablespoons ground flax meal, divided
    • 4 tablespoons water, divided
  • 1 cup fresh zucchini, grated

Other Ingredients:

  • 1/31/2 cup dairy-free chocolate chips
  • 1 tablespoon plant-based butter, melted


  1. Preheat oven to 375 degrees F.
  2. Place paper muffin liners in a 12 muffin tin and spray with olive oil. Set aside.
  3. Take two small bowls and make two flax eggs by adding 1 tablespoon of ground flax meal to each bowl and then 2 tablespoons of water to each small bowl. Stir to mix the flax and water together and then set aside for at least 5 minutes.
  4. Grate the zucchini and squeeze out as much excess water as possible using either your hands, paper towel or cheese cloth (don’t skip this part!). Set aside.
  5. Combine Dry Ingredients in a medium mixing bowl. Stir to combine with a fork or whisk to ensure no lumps and that everything combines well. Set aside.
  6. In a large bowl, add applesauce, mashed banana and almond milk.  Stir to combine.
  7. Add the two flax eggs to the applesauce mixture and mix gently for just a few seconds.
  8. Add the zucchini to the applesauce mixture and gently mix for a few more seconds.
  9. Pour the Dry Ingredients a little at a time into the Wet Ingredients and stir to combine.
  10. Once the wet and dry ingredients are fully combined (don’t over-mix) add the chocolate chips and melted plant based butter.
  11. Stir to combine, again being careful to not over-stir.
  12. Scoop dough into muffin liners, filling almost to the top (they will rise a bit).
  13. Bake in the preheated oven for 32 minutes or until a toothpick comes out clean.
  14. Let cool for 2-3 minutes and then carefully remove and place on a cooling rack as soon as possible.
  15. Let fully cool before serving.


  • Spray with olive oil (or nonstick cooking spray): definitely remember to spray the muffin tin liners or the muffins will stick!
  • Flax Eggs Separately: we have had better luck making them in separate bowls instead of all in one bowl.
  • Flax Egg Substitutions: this recipe works great with regular eggs too!
  • Let cool!: Make sure you let these fully cool! If you break them open before they are fully cool they may look a little mushy in the very center.  Once they have cooled they will be fluffy and delicious!


  • Serving Size: 1 muffin
  • Calories: 156
  • Sugar: 12.4 g
  • Sodium: 188.7 mg
  • Fat: 2 g
  • Carbohydrates: 27.9 g
  • Protein: 2.3 g
  • Cholesterol: 2.5 mg