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5 from 1 vote

Healthy Cupcakes (Carrot with Cream Cheese Frosting)

Irresistibly moist and fluffy, these delicious healthy cupcakes are made with carrots, applesauce and warming spices like cinnamon and nutmeg. They can be made with one bowl, prepped ahead and only take 25 minutes to prepare! Top them with my healthier cream cheese frosting for a delicious breakfast, snack or a secretly healthy treat that everyone will love.
Prep Time10 mins
Cook Time15 mins
0 mins
Total Time25 mins
Course: healthy, lunchbox, Snack
Cuisine: Australian
Servings: 10
Calories: 226kcal


For the carrot cupcakes

  • 1 ½ cups plain white whole wheat flour or white flour
  • 1 tsp baking powder
  • 2 flat tsp ground cinnamon
  • ½ tsp ground ginger
  • ¼ tsp nutmeg
  • pinch salt
  • 1 cup finely grated carrot
  • 1 egg for egg free cupcakes, use an extra ¼ cup of applesauce instead
  • cup applesauce
  • 2 tsp vanilla vanilla bean paste or essence
  • ¼ cup olive oil
  • cup crushed pineapple leave a little juice in the pineapple
  • ½ cup maple syrup

For the healthy cream cheese frosting

  • 1 cup cream cheese 250 grams. Use regular or light cream cheese, softened at room temperature.
  • 2 tbsp lemon juice
  • 1 tsp vanilla
  • maple syrup to taste approx ¼ cup


For the cupcakes

  • Pre-heat oven to 180 °C. Line a cupcake tray (10-12 holes) with patty cases, or coat with a light oil spray. **You can also make mini or larger muffins, but the cooking times will vary.
  • Mix all of the dry ingredients in a bowl (flour, baking powder, spices, salt) together with the grated carrot.
  • Add the remaining wet ingredients and stir until just combined. Evenly divide the mixture into the prepared cupcake tray and bake for around 15 minutes, or until the cupcakes are completely cooked through. Transfer to a wire rack to cool completely.

For the cream cheese frosting

  • Combine all of the frosting ingredients into a bowl and beat with an electric mixer until smooth and combined.
  • Pipe or spread the frosting over the cooled cupcakes and decorate with any desired toppings. The cupcakes will keep in the fridge for 4-5 days. Enjoy!


  • Try adding some of your favourite add-ins to the mixture before baking. Ingredients like finely chopped walnuts, shredded coconut and raisins all make tasty additions! You can also top the cream cheese frosting with some walnuts or blueberries.
  • For vegan carrot cupcakes, you just need to make a couple of super simple swaps! Swap the egg for an extra ¼ cup applesauce or olive oil and use vegan cream cheese instead of regular cream cheese for the frosting.
  • The mixture can also be adapted to make larger muffins or mini cupcakes. For whole wheat carrot muffins, use a larger muffin tray. The cooking time below is designed for 10 medium sized cupcakes and will vary for larger or smaller sizes.
  • Make a double batch and keep some (unfrosted) in the freezer for a convenient snack.
  • For keto cream cheese frosting, you can use stevia or other keto-approved sweeteners instead of maple syrup.
  • Ensure that the cream cheese for the frosting is softened at room temperature before beating. Cold cream cheese will make the frosting lumpy.
  • Whole wheat flour – white whole wheat (wholemeal) flour or unbleached flour have the same benefits as whole wheat flour, but is much lighter in taste and texture. And it also means that the flour is made entirely with whole grains. White flour can also be used, or a mix of white and wholemeal. For gluten free cupcakes, try a plain (all purpose) gluten-free flour.
  • Applesauce – applesauce is such a great ingredient! It naturally sweetens baking recipes and can also be used as an egg replacement if you need to be egg-free or vegan-friendly. Applesauce also provides extra moisture without having to use as much oil. You can use homemade, steamed and pureed apples, or unsweetened applesauce can be found in supermarkets and health food stores.


Calories: 226kcal | Carbohydrates: 30g | Protein: 5g | Fat: 10g | Saturated Fat: 3g | Cholesterol: 29mg | Sodium: 131mg | Potassium: 274mg | Fiber: 3g | Sugar: 14g | Vitamin A: 2295IU | Vitamin C: 3mg | Calcium: 91mg | Iron: 1mg