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Apple muffins topped with cinnamon sugar on a cooling rack.

Healthy Apple Cinnamon Muffins

  • Author: Brittany Mullins
  • Prep Time: 15 minutes
  • Cook Time: 35 minutes
  • Total Time: 50 minutes
  • Yield: 12


These healthy apple cinnamon muffins are made with a blend of whole wheat and all-purpose flour. They’re loaded with fall flavor and extra moist thanks to pumpkin! Vegan modifications included.


  • 1/4 cup (4 Tablespoons) butter, softened*
  • 3/4 cup coconut sugar or brown sugar
  • 3/4 cup plain non-fat Greek yogurt*
  • 3/4 cup canned pumpkin
  • 2 Tablespoons ground flaxseed + 6 Tablespoons water (or 2 regular eggs)
  • 1 teaspoon vanilla
  • 1 cup all-purpose flour
  • 1 cup whole wheat flour
  • 1 teaspoon baking powder
  • 1 teaspoon baking soda
  • 1/2 teaspoon cinnamon
  • 1/4 teaspoon sea salt
  • 1 1/2 cups peeled and finely chopped apple pieces (about 12 apples)


  • 2 Tablespoons coconut sugar or dark brown sugar
  • 1 teaspoon cinnamon


  1. Preheat oven to 350°F. Line a muffin pan with cupcake liners or coat with cooking spray.
  2. In a small bowl, whisk together the 2 Tablespoons of ground flaxseed with the 6 Tablespoons of water and let sit while you start preparing the other ingredients.
  3. In a small bowl, mix together the topping – 2 Tablespoons of sugar with 1 teaspoon cinnamon.
  4. In a medium bowl, whisk together the all-purpose and whole wheat flour, baking soda, baking powder, cinnamon and salt.
  5. In a large bowl, mix the 3/4 cup sugar with the softened butter until combined. Add the flaxseed/water mixture, pumpkin and vanilla. Stir in yogurt.
  6. Fold the flour mixture into the wet mixture. Gently stir in the apple chunks.
  7. Pour the batter into the prepared muffin pan and sprinkle with the brown sugar topping. Bake for 25 to 30 minutes or until a wooden pick inserted in center of 1 of the muffins comes out clean.
  8. Let cool on a wire rack for 15 minutes. Store any leftover muffins in the refrigerator for up to 3-4 days.


  • For vegan muffins: use Earth Balance Buttery Stick instead of butter and coconut milk yogurt instead of regular Greek yogurt.
  • Category: Breakfast
  • Method: Bake
  • Cuisine: American


  • Serving Size: 1 muffin
  • Calories: 185
  • Sugar: 13g
  • Fat: 5g
  • Carbohydrates: 31g
  • Fiber: 4g
  • Protein: 5g

Keywords: healthy apple muffins

Parchment paper lined with protein balls.


Eating healthy doesn’t have to be boring!