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Healthy Chocolate Chip Muffins

Want a delicious Chocolate Chip Muffin with zero guilt?  Give these Healthy Chocolate Chip Muffins a try!  Made with yogurt, applesauce, flax, and quinoa flour, these are muffins you can feel good about giving the kids.
Course Snack
Cuisine Quinoa
Keyword Healthy Chocolate Chip Muffins
Prep Time 10 minutes
Cook Time 1 hour
Servings 12
Calories 313kcal
Author Wendy Polisi


  • 3 cups all purpose gluten free flour blend
  • 1 teaspoon baking powder
  • ½ teaspoon sea salt
  • 1 cup cooked quinoa
  • 1 cup coconut palm sugar or sweetener of choice
  • 1/3 cup maple syrup or agave nectar
  • ½ cup applesauce
  • 3 tablespoons coconut oil melted
  • 1 cup milk of choice at room temperature
  • 1 cup almond plain yogurt or low fat
  • 2 flax or room temperature eggs
  • 1 ½ teaspoon vanilla extract
  • 1 cup chocolate chips


  • Preheat oven to 350 degrees. Line a 12 cup muffin tin with paper baking cups. Spray lightly with olive oil spray. If using flax eggs, combine 2 tablespoons ground flax seeds plus 6 tablespoons warm water.
  • In a large bowl, sift together flour, baking powder and sea salt. Stir in cooked quinoa.
  • In a separate bowl whisk together coconut palm sugar, maple syrup, apple sauce, melted coconut oil, milk, yogurt, (flax) eggs and vanilla extract. Add wet ingredient to the dry ingredients and stir until just combined. Stir in chocolate chips.
  • Using a measuring spoon or ice cream scoop, fill the muffin cups. Bake until golden brown, about 30 to 35 minutes. Let cool in the pan on a rack for 20 minutes. Separate tops with a knife if necessary. Invert and remove muffins from the pan.


Variations for Healthy Chocolate Chip Muffins

  • If you aren’t gluten free, save yourself the expense of gluten free flours and substitute 2 ¼ cups all purpose flour plus ¾ cup toasted quinoa flour.

Tips for Making Chocolate Chip Muffins

  • If you are gluten free, I do recommend freezing them and reheating in the oven when you are ready to eat. Gluten free baked goods just don't keep like conventional ones.


Calories: 313kcal | Carbohydrates: 56g | Protein: 5g | Fat: 8g | Saturated Fat: 5g | Cholesterol: 2mg | Sodium: 165mg | Potassium: 87mg | Fiber: 4g | Sugar: 26g | Vitamin A: 35IU | Vitamin C: 2.7mg | Calcium: 114mg | Iron: 1.5mg