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Whole wheat chocolate chip muffins lined up on a cooling rack.

Whole Wheat Dark Chocolate Chip Muffins

These super moist Whole Wheat Dark Chocolate Chip Muffins are made up of 100% stone ground whole wheat and chunks of dark chocolate for a healthier way to treat yourself.
Course Breakfast, Dessert, Snack
Keyword breakfast, chocolate chips, Dessert, muffins, Snack, unrefined sugar, whole wheat
Prep Time 10 minutes
Cook Time 25 minutes
Total Time 35 minutes
Servings 12 muffins
Author Dana Sandonato


  • Muffin tray
  • Muffin cups


  • 2 cups 100% stone ground whole wheat flour
  • 1 cup unrefined sugar I used coconut palm sugar
  • 2 tsp baking soda
  • 1 TBSP ground cinnamon
  • 1/2 tsp kosher salt
  • 2 large eggs
  • 1/2 cup extra virgin olive oil
  • 1/2 cup unsweetened apple sauce
  • 2 tsp vanilla extract
  • 1 large apple, peeled and grated (about 1.5 cups worth of grated apple)
  • 1 cup dark chocolate chips
  • 1/2 cup toasted shredded coconut You can omit this entirely, or substitute with chopped nuts or dried fruit, like cranberries.


  • Preheat oven to 350º F. Line a muffin tray with paper muffin cups.
  • In a large bowl, whisk together the flour, sugar, baking soda, cinnamon, and salt; set aside.
  • In another bowl, whisk together the eggs, olive oil, applesauce, and vanilla extract. Once cohesive, gently stir in the grated apple, chocolate chips, and toasted coconut if using. (Or your substitution.)
  • Slowly add the dry ingredients to the wet ingredients, stirring constantly, until everything is well combined.
  • Spoon the mixture into the paper cups right up to the tops of the cups.
  • Bake for 20-25 minutes, or until a cake tester/toothpick comes out clean when tested.