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healthy carrot pumpkin muffins with cream cheese frosting
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4.89 from 9 votes

Healthy Carrot Pumpkin Muffins with Cream Cheese Frosting

These muffins are loaded with vitamins, minerals and fiber thanks to the pumpkin puree, carrots and whole wheat flour, plus tons of other goodies! The cream cheese "frosting" is the cherry on top, and it's healthy enough that you can still get away with eating these babies for breakfast. Muffins or cupcakes? YOU decide. ;)
Prep Time15 mins
Cook Time15 mins
Total Time30 mins
Course: Breakfast, Dessert
Cuisine: American
Keyword: carrot cake, cream cheese frosting, cupcakes, healthy breakfast, healthy carrot pumpkin muffins, healthy recipe, meal prep, muffins
Servings: 18 muffins
Calories: 160kcal


  • 2 cups whole wheat flour
  • 1 Tbsp baking powder
  • 1 tsp baking soda
  • 2 tsp ground cinnamon
  • 1/2 tsp ground ginger
  • 1/4 tsp ground nutmeg
  • Pinch of salt ~1/8 tsp
  • 2 eggs
  • 1 cup pumpkin puree
  • 1/2 cup plain Greek yogurt
  • 1/2 cup unsweetened applesauce
  • 1/4 cup maple syrup
  • 1/4 cup unsweetened vanilla almond milk
  • 3 Tbsp coconut oil melted and cooled
  • 1 cup finely shredded carrots 2-3 large carrots, shredded in food processor
  • 1 tsp vanilla extract

Optional Mix-Ins:

  • 1/3 cup chopped walnuts
  • 1/3 cup white chocolate chips

Cream Cheese Frosting

  • 1/2 cup plain whipped cream cheese
  • 1/2 cup plain Greek yogurt
  • 1/2 tsp cinnamon
  • 1/2 tsp vanilla extract
  • 2 tsp honey


  • Preheat oven at 350° F. Grease two muffin pans with non-stick cooking spray. (Mine made 18 muffins)
  • Peel large carrots and chop into 2 inch chunks. Place in food processor and pulse until finely shredded. Repeat until you have 1 cup of shredded carrot. I used 2-3 large carrots.
  • In a large bowl, combine dry ingredients: whole wheat flour, baking powder, baking soda, cinnamon, ginger, nutmeg, and salt. Set aside.
  • In a medium bowl, beat 2 eggs. Add Greek yogurt, maple syrup, coconut oil, pumpkin puree, unsweetened applesauce, unsweetened vanilla almond milk, vanilla extract, and shredded carrots. Mix well.
  • Pour wet ingredients into dry ingredients. Add additional mix-ins as desired, including chopped walnuts and white chocolate chips. Stir until just combined. Do not over-mix. Pour batter evenly into prepared muffin cups.
  • Bake for 13-15 muffins, or until a knife inserted in the center comes out clean.
  • While muffins are baking, prepare cream cheese frosting by combining cream cheese, Greek yogurt, cinnamon, vanilla and honey in a small bowl. Mix well. Let muffins cool for 15-20 minutes before adding frosting.
  • Store in the refrigerator for 3-5 days in an airtight container, or transfer to the freezer in freezer-safe bags. Reheat in the microwave to thaw. If not adding frosting, serve with a dollop of almond butter on top, if desired.


Calories: 160kcal | Carbohydrates: 19g | Protein: 4g | Fat: 7g | Saturated Fat: 4g | Cholesterol: 26mg | Sodium: 115mg | Potassium: 231mg | Fiber: 2g | Sugar: 7g | Vitamin A: 3415IU | Vitamin C: 1.1mg | Calcium: 82mg | Iron: 1mg