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Two healthy chocolate chip muffins stacked on top of each other. They are wrapped in a paper liner.
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5 from 10 votes

Healthy Chocolate Chip Muffins

These healthy chocolate chip muffins are soft, fluffy, perfectly moist and absolutely delicious. They're made with whole wheat flour, Greek yogurt, maple syrup and studded with chocolate chips.
Prep Time15 minutes
Cook Time20 minutes
Total Time35 minutes
Course: Breakast
Cuisine: American
Keyword: healthy chocolate chip muffins
Servings: 12



  • Preheat oven to 350°F. Line a 12 cup muffin pan with paper or silicone liners.
  • Whisk almond milk and apple cider vinegar in a medium bowl and let curdle for 5-10 minutes. Set aside.
    Almond milk and apple cider vinegar whisked together.
  • In a large bowl combine flour, baking powder, baking soda, cinnamon and salt.
    Flour, baking powder, baking soda, cinnamon and salt combined in a large bowl.
  • In the same bowl as milk, add eggs, maple syrup, Greek yogurt, coconut oil and vanilla extract. Whisk until combined.
    Two eggs, maple syrup, Greek yogurt, coconut oil and vanilla extract added to the bowl with milk and apple cider vinegar.
  • Pour the wet ingredients into the bowl with the dry ingredients and stir until just combined. Don’t overmix!
    Wet ingredients being poured into a mixing bowl with dry ingredients.
  • Fold in chocolate chips and evenly divide the batter evenly between the 12 muffin cups. Top with extra chocolate chips.
    Batter poured evenly into 6 paper lined muffin tins.
  • Bake for 20-22 minutes or until a toothpick inserted in the center of the muffin comes out clean.
    Twelve chocolate chip muffins in a muffin tin.
  • Let muffins cool in the tin for a few minutes, then remove so they don’t continue to cook and let cool completely on a wire rack.


  • Whole wheat pastry flour: If you can’t find whole wheat pastry flour you can also use white whole wheat flour, a blend of all-purpose and regular whole wheat flour or just regular all-purpose flour.
  • Greek yogurt: Any yogurt will work here!
  • Maple syrup: You can use agave, honey or even monk fruit maple syrup as a substitute for maple syrup. 


Serving: 1muffin | Calories: 225kcal | Carbohydrates: 34g | Protein: 5g | Fat: 11g | Saturated Fat: 8g | Monounsaturated Fat: 1g | Cholesterol: 39mg | Sodium: 208mg | Potassium: 96mg | Fiber: 4g | Sugar: 20g