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The Best Carrot Cake Cupcakes

By Lori, Last updated on September 3, 2025
The links in the post below may be affiliate links. Read the full disclosure.

I’m sharing this wonderful Carrot Cake Cupcake recipe, which is sure to become one of your family favorites! It’s easy to follow and can be made any time of year.

The Best Carrot Cake Cupcakes

This is one of my absolute favorite cupcake recipes. Thanks to their wet ingredients, these moist cupcakes are packed with flavor. Molasses, generous amounts of ground spices, applesauce, and fresh carrots add the perfect amount of moisture. One of the best parts of these homemade carrot cake cupcakes is the cream cheese frosting that ties it all together.

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Prep time: 20 minutes Cook time: 20 minutes Yields: 24 cupcakes

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Ingredients for Carrot Cake Cupcakes

For the Carrot Cupcakes

  • 1 c. whole pecans, divided
  • 4 large eggs, room temperature
  • 1 c. vegetable oil
  • 1 c. brown sugar, tightly packed
  • ¾ c. white sugar
  • 3 T. molasses
  • 1 c. unsweetened applesauce
  • 2 t. real vanilla extract
  • 2½ c. all-purpose flour
  • 2 t. baking powder
  • 1 t. baking soda
  • ½ t. salt
  • 2 t. ground cinnamon
  • 1 t. ground ginger
  • ½ t. ground nutmeg
  • ½ t. t. ground cloves
  • 2 c. fresh finely shredded carrots (approximately 5-6 medium carrots)

For the Homemade Cream Cheese Frosting

  • 8 oz. cream cheese, room temperature
  • 4 T. unsalted butter, room temperature
  • 1 t. real vanilla extract
  • ¼ t. salt
  • 1¾ c. powdered sugar

Supplies Used

  • Box grater
  • Airtight container
  • 24 paper liners
  • 2 12-cup muffin tins

How to Make The Best Carrot Cake Cupcakes

#1. Arrange both oven racks at an equal distance apart. Preheat the oven to 350°F and line two 12-cup muffin tins with cupcake liners to perfect the cupcake form. Set aside.

#2. Finely chop three-quarters of the pecans and place in a skillet set over medium heat. Toast the chopped pecans, stirring frequently, until fragrant but not overly brown. Remove from heat and set aside in a medium bowl. Note: Reserve the remaining quarter cup of whole pecans for garnish.

#3. Whisk together the eggs and vegetable oil in a large bowl. Add the brown sugar, white sugar, molasses, applesauce, and vanilla extract and continue whisking until combined.

carrot cake cupcake batter process

#4. In a separate bowl, combine the flour, baking powder, baking soda, salt, cinnamon, ginger, nutmeg, and cloves. Stir to combine.

#5. Gradually add some of the dry ingredients to the wet and whisk to combine. Repeat until all the dry ingredients have been incorporated into the batter.

#6. Pour the toasted pecans into the large mixing bowl and stir to combine.

#7. Add the freshly grated carrots and carefully fold into the mixture until thoroughly incorporated into the batter.

#8. Fill each cupcake liner with the cupcake batter until approximately three-quarters full, as shown. Note: Do not overfill.

Place the muffin tin into the preheated oven for 18-20 minutes or until a toothpick inserted in the center comes out clean. Note: Rotate the muffin pans to the other rack halfway through baking.

Remove from oven and transfer the cupcakes to the wire rack to cool completely.

Remaining Steps for the Frosting Recipe

#9. While the cupcakes are cooling, prepare the frosting by beating together the cream cheese, butter, vanilla extract, and salt. Slowly add the powdered sugar a little at a time until thoroughly incorporated into the frosting. Set aside.

cream cheese frosting process

#10. Once the unfrosted cupcakes are completely cool, frost them with the cream cheese frosting. If desired, garnish these delicious cupcakes with the remaining whole pecans and place them at the center of a cupcake. Enjoy!

The Best Carrot Cake Cupcake

Kitchen Tip

  • For leftovers, place the remaining cupcakes in a deep, airtight, freezer-safe container and store at room temperature for 3-4 days or freeze for up to 3 months.

Don’t forget to share these delicious Carrot Cake Cupcakes with your friends and loved ones! Follow me on social media to stay updated on my latest recipes.

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        More Recipes To Try

        If you have a sweet tooth and are a fan of this Carrot Cake Cupcakes recipe, try these other delicious desserts:
        • Orange Glazed Carrots
        • Cherry Almond Clafoutis
        • Strawberry Chocolate Muffins
        • 11 Favorite Carrot Cake Recipes
        • Chocolate Covered Strawberries

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        Don’t forget to share this Best Carrot Cake Cupcakes recipe with your friends and loved ones. If you are on social media, I would love to connect with you on Facebook, Instagram, Pinterest, or Twitter. Just click on the links to visit my profile. Leave a message and I will follow you back! Click here to see all my recipes.
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