Cream Cheese-Filled Carrot Cake Cupcakes are rich and moist carrot cupcakes filled with a surprise cream cheese center! You still get the flavors of a cream cheese frosted carrot cake with each bite, but with the ‘frosting’ inside! If you prefer the frosting on top, I also have Carrot Cake Cupcakes with the Best Cream Cheese Frosting you will love!

Cream Cheese Filled Carrot Cake Cupcakes on a White Counter With One Halved Showing Cream Cheese Inside.
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Ingredients & Substitutions

Cream Cheese Filling: The filling is a sweet and creamy ‘frosting’ made with cream cheese and confectioners’ sugar.

Spices: When it comes to achieving the classic flavor of carrot cake, ground cinnamon and nutmeg are commonly used spices. So, I couldn’t leave those out of these cupcakes!

Nuts: I love adding walnuts to my carrot cake recipes. For even more flavor, add my candied walnuts! Of course, you could leave them out if preferred. Pecans are another popular choice to add to carrot cake.

Carrots: I recommend using freshly grated carrots for the most moisture in the cupcakes. You will need about 2 1/4 cups of grated carrots to go into the cupcake batter. You could substitute pre-shredded carrots, but that may affect the final product.

Pineapple: While it’s not a necessary ingredient, I personally enjoy adding pineapple to my carrot cake because it adds moisture and enhances the overall flavor and texture of the cake.

Steps for Adding Batter, Cream Cheese, and More Batter to Make Cream Cheese Filled Carrot Cake Cupcakes.

Can I Make Carrot Cake Cupcakes Ahead of Time?

Yes! You can get the filling mixed together and the cupcake batter made ahead of time. The filling can be stored in the refrigerator for up to 3-4 days. Give it a stir before adding it to the cupcakes. The cupcake batter can be mixed together the night before (without the nuts). Store it in an airtight container in the refrigerator for up to 24 hours. When ready, fold in the nuts and let the batter come to room temperature before assembling and baking the cupcakes.

Cream Cheese Filled Carrot Cake Cupcakes Stacked and Surrounded by More Cupcakes.

Can I Make The Cupcakes Without the Cream Cheese Filling?

Sure! If you prefer just the carrot cake cupcakes without the cream cheese filling, simply leave it out! Then, it’s all about what you call them…are they now carrot cake muffins? Debate amongst yourselves…

Hand Holding Cream Cheese Filled Carrot Cake Cupcakes.

How to Store Cream Cheese-Filled Carrot Cake Cupcakes

After baking carrot cupcakes with a cream cheese center, it’s important to let them cool completely before storing them. Once cooled, transfer them to an airtight container and refrigerate for up to 3-4 days. If you want to store them for longer, freeze them for 2-3 months instead. To enjoy them later, thaw the cupcakes in the refrigerator overnight.

Cream Cheese Filled Carrot Cake Cupcakes on a White Surface Surrounded by More Cupcakes.

Cream Cheese Filled Carrot Cupcakes

Prep Time 20 minutes
Cook Time 24 minutes
Total Time 44 minutes
Cream Cheese-Filled Carrot Cake Cupcakes are rich and moist carrot cupcakes filled with a surprise cream cheese center!


Cream Cheese Filling

  • 8 ounces cream cheese, room temperature
  • 1 cup (125 g) confectioners' sugar


  • 2 cups (400 g) granulated sugar
  • 1 ¼ cups (272.5 g) vegetable oil
  • 1 teaspoon vanilla extract
  • 3 large eggs, room temperature
  • 2 ¾ cups (344 g) all-purpose flour
  • 2 teaspoons ground cinnamon
  • ¼ teaspoon nutmeg
  • 2 teaspoons baking soda
  • 1 ½ teaspoons kosher salt
  • 1 cup roughly chopped walnuts
  • 2 ¼ cups (247.5 g) finely grated carrots
  • ½ cup crushed pineapple


Cream Cheese Filling

  • Using a stand mixer with the paddle attachment beat together the cream cheese and confectioners' sugar.
  • Place the cream cheese mixture in the refrigerator as you make the cupcake batter.


  • Preheat the oven to 350°F. Line 2 muffin tins with paper liners. (This recipe will make 20 cupcakes.)
  • To the bowl of a stand mixer, add the sugar, oil, vanilla, and eggs. Mix on medium-low speed until the mixture is light yellow, about 3 minutes.
  • In a separate bowl sift together flour, cinnamon, nutmeg, baking soda, and salt. 
  • With the mixer on low speed, slowly and gently add in the dry ingredients. Mix until JUST combined.
  • Continuing to mix on low, add the nuts, carrots, and pineapple.


  • Remove the cream cheese filling from the refrigerator.
  • Add 2 tablespoons of batter to each of the lined muffin cups.
  • Top the cupcake batter with a heaping teaspoon of the cream cheese filling.
  • Add 3 tablespoons of the cupcake batter on top of the cream cheese filling.
  • Bake for 24 minutes, or until golden brown.
  • Transfer the muffin tins to a wire rack to cool for a few minutes before gently removing the cupcakes from the muffin tin to cool completely.

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What the Test Kitchen had to say about this recipe:


Cream cheese makes everything better. Right? Carrot cake is one of my favorite things and the cream cheese filling in this cupcake takes it to the next level!


What a fantastic and delicious twist to a traditional cream cheese-frosted carrot cake. The 'frosting' is INSIDE! You get the moist cupcake with all the flavors in carrot cake, but in a hand-held cupcake. Genius!


I like the idea of adding the filling inside the cupcake. I had never tried a cupcake with cream cheese inside, so it was good to give this a try. This has a very soft and moist texture. The carrot cake flavor is there and it is great!


A classic carrot cake cupcake with just a hint of cream cheese is just perfect. I love that you could technically eat it as a muffin without guilt! I also love that the filling inside keeps a moist cupcake even more moist!


I LOVE carrot cake!! Our version is so moist and tender! The filling on the inside is a sweet surprise and a fun addition to an already incredible treat!

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Meet Amanda Rettke

Amanda Rettke is the creator of I Am Baker, and the bestselling author of Surprise Inside Cakes: Amazing Cakes for Every Occasion – With a Little Something Extra Inside.Over the course of her 15+ year blogging adventure, she has been featured in and collaborated with the Food Network, New York Times, LA Times, Country Living Magazine, People Magazine, Epicurious, Brides, Romantic Homes, life:beautiful, Publishers Weekly, The Daily Mail, Star Tribune, The Globe and Mail, DailyCandy, YumSugar, The Knot, The Kitchn, and Parade, to name a few.

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