Healthier Pumpkin Chocolate Chip Muffins


For the Muffins:

  • 2 ½ cups whole wheat flour
  • ½ TBSP pumpkin spice
  • 1 TBSP ground cinnamon
  • 2 tsp baking soda
  • 1 tsp baking powder
  • 1 cup canned pumpkin
  • ½ cup brown sugar
  • 1 cup unsweetened applesauce
  • ¼ cup honey
  • 1 cup Greek yogurt
  • 2 large eggs, room temp
  • 1 tsp vanilla extract
  • ½ cup coconut oil melted and cooled
  • 1 cup chocolate chips (divided)

For the Optional Glaze:

  • 1 cup powdered sugar
  • 2 TBS milk (I used oat milk)
  • ½ teaspoon vanilla extract


  1. Preheat the oven to 350F. Grease two muffin/cupcake tins or line with paper liners. Set aside.
  2. In a medium bowl combine dry ingredients and set aside.
  3. In a large bowl whisk together pumpkin, sugar, applesauce and honey, Greek yogurt, eggs, vanilla and melted/cooled coconut oil. 
  4. Add the dry ingredients to the wet ingredient mixture by gently folding in using a spatula or mix on low speed with an electric mixer.
  5. Fold in 3/4 cup of chocolate chips with spatula. 
  6. Spoon batter in greased muffin tins about ¾ of the way full. Top the batter with the remaining 1/4 cup of chocolate chips (a few on each muffin.) Bake for 20-22 minutes or until a toothpick inserted into the center of the muffins comes out clean.
  7. Allow muffins to cool in the tins for about 25 minutes before removing. 
  8. For optional glaze: Sift the powdered sugar into a medium bowl. Whisk in milk and vanilla extract. Drizzle glaze on top of each muffin. Serve and enjoy!


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