Healthy Pumpkin Muffins ona white plate with a pumpkin in the background.
Print Pin
4.58 from 7 votes

Healthy Pumpkin Carrot Apple Muffins

Tender, lightly spiced pumpkin muffins filled with shredded apples and carrots. Similar to pumpkin bread and carrot cake - but healthier!
Course Breakfast, Dessert, Snack
Cuisine American
Prep Time 20 minutes
Cook Time 15 minutes
Total Time 35 minutes
Servings 15 -18
Calories 187kcal
Author Allison - Celebrating Sweets



  • 1 cup all purpose flour
  • 1 cup white whole wheat flour
  • 1/4 cup wheat bran, ground flaxseed or old fashioned oats
  • 2 teaspoons baking powder
  • 1 teaspoon baking soda
  • 1/2 teaspoon salt
  • 2 1/2 teaspoons ground cinnamon or pumpkin pie spice
  • 1/2 cup brown sugar packed
  • 2 eggs
  • 1 cup pumpkin puree not pumpkin pie filling
  • 1/4 cup melted coconut oil or canola oil
  • 1/2 cup unsweetened applesauce
  • 1 1/2 cups grated carrots (see note)
  • 1 1/2 cups grated apple (see note)
  • 1/2 cup raisins or chopped walnuts optional

Cream Cheese Frosting (optional):

  • 2 ounces reduced fat cream cheese softened
  • 1 tablespoon unsalted butter softened
  • 3/4 cup powdered sugar
  • 1/4 teaspoon vanilla extract
  • 1-2 teaspoons skim milk


  • Preheat oven to 375°. Grease 15-18 muffin cups. Set aside
  • In a medium bowl, whisk together flours, wheat bran/flaxseed/oats, baking powder, baking soda, salt, cinnamon, and brown sugar.
  • In a large bowl, whisk eggs, pumpkin puree, oil, and applesauce until combined.
  • Stir the flour mixture into the wet ingredients, mixing until just combined. Add carrots, apple, and raisins and stir until evenly distributed, being careful not to over mix.
  • Evenly divide the batter between muffin cups, filling about 2/3 full. Bake for 15-20 minutes, until a toothpick inserted into the center of the muffins comes out without raw batter on it. Cool in muffin pan for 10 minutes, then remove muffins from the pan to continue cooling.


  • With a hand mixer or stand mixer, beat cream cheese and butter until smooth and creamy. Add powdered sugar, vanilla, and 1 teaspoon of milk. Beat for about 1 minute, until smooth. Add more milk of necessary. Drizzle frosting over the top of cooled muffins (I placed the frosting in a plastic bag, snipped the corner, and squeezed it onto the muffins).


I grate the apples on the medium holes of a box grater, and the carrots on the fine holes of a box grater.
Recipe adapted from Williams Sonoma


Calories: 187kcal | Carbohydrates: 31g | Protein: 3g | Fat: 5g | Saturated Fat: 1g | Cholesterol: 25mg | Sodium: 189mg | Potassium: 204mg | Fiber: 2g | Sugar: 16g | Vitamin A: 4765IU | Vitamin C: 2.1mg | Calcium: 55mg | Iron: 1.2mg