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Healthy Whole Wheat Blueberry Breakfast Cupcakes

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  • Author: Maegan - The BakerMama
  • Prep Time: 10 mins
  • Cook Time: 15 mins
  • Total Time: 25 mins
  • Yield: 12
  • Category: Breakfast


Cupcakes for breakfast?! Yes, please! No butter, oil or refined sugar needed to make these hearty, Healthy Whole Wheat Blueberry Breakfast Cupcakes that are bursting with blueberries and topped with a dreamy, creamy 3-ingredient frosting.



  • 2 cups whole wheat flour
  • 1 teaspoon baking powder
  • 1 teaspoon baking soda
  • 1 teaspoon cinnamon
  • 1/4 teaspoon kosher salt
  • 2 large eggs, lightly beaten
  • 1 cup milk
  • 1/2 cup pure maple syrup
  • 1 teaspoon vanilla
  • 11/2 cups fresh or frozen blueberries

Maple Cream Cheese Frosting:

  • 1 (8 ounce) package cream cheese, softened (I use 1/3 less fat cream cheese)
  • 3 tablespoons plain or vanilla-flavored Greek yogurt
  • 2 tablespoons pure maple syrup


  1. Preheat oven to 350°F. Line a 12-cup cupcake pan with cupcake liners and spray with non-stick cooking spray.
  2. In a large mixing bowl, whisk together the flour, baking powder, baking soda, cinnamon and salt. Make a well in the center of the flour mixture and add the eggs, milk, maple syrup and vanilla. Whisk until mixture is thick and well combined. Gently fold in the blueberries with a spatula or wooden spoon.
  3. Divide mixture evenly among prepared cupcake liners, filling each one about 2/3 full. Bake for 13-15 minutes or until a toothpick inserted in the center of the cupcakes comes out with a few crumbs on it. Let cupcakes cool in pan for 10 minutes before transferring to a wire rack to cool completely.
  4. To make the frosting, beat the cream cheese, Greek yogurt and maple syrup with a hand mixer (or in the bowl of an electric mixer fitted with the whisk attachment) on medium speed until smooth and spreadable, scraping the sides of the bowl as needed.
  5. Once cupcakes are cool, frost each cupcake with the maple cream cheese frosting.