Healthy Chocolate Muffins

5 from 11 reviews

Healthy chocolate muffins recipe with greek yogurt, applesauce, whole wheat flour, cacao powder and honey. Kids absolutely love these fudgy and nutritious muffins.

  • Author: Olena of
  • Prep Time: 5 minutes
  • Cook Time: 25 minutes
  • Total Time: 30 minutes
  • Yield: 12 muffins 1x
  • Category: Dessert
  • Method: Oven
  • Cuisine: North American


  • 2 large eggs*
  • 1 cup applesauce, unsweetened
  • 1/2 cup Greek or regular (2%+ fat) yogurt, plain
  • 1/2 cup + 2 tbsp maple syrup or honey
  • 1/3 cup cacao powder
  • 2 tsp baking powder, aluminum free
  • 1 tsp baking soda
  • 1/4 tsp salt
  • 1 3/4 cups whole wheat flour
  • 1/2 cup chocolate chips
  • Cooking spray (I use Misto)


  1. Preheat oven to 350 degrees F and spray silicone muffin tin with cooking spray. Set aside.
  2. In a medium mixing bowl, whisk eggs for 15 seconds. Add applesauce, yogurt, maple syrup and whisk to combine. Add cacao powder, baking powder, baking soda, and salt; whisk thoroughly until smooth and no lumps.
  3. Add flour and gently mix with spatula just enough to combine. Do not over mix, let batter sit for a few seconds, then stir again. Add chocolate chips and give a few gentle stirs to incorporate.
  4. Distribute batter evenly between 12 openings of a tin (I used regular ice cream scoop) and bake on a third-fourth rack from the bottom (farther away from heat) for 25 minutes or until a toothpick inserted in the centre comes out clean. Let muffins cool for about 5 minutes and transfer to a cooling rack to cool off completely.

Store: Refrigerate in an airtight container for up to 1 week or freeze for up to 3 months.


*One time I ran out of eggs and used 1 large egg + 3 tbsp ground flax seed diluted in 6 tbsp warm water which makes a vegan egg replacer. Very moist and fudgy results – try that.

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