Cream Cheese Carrot Cake Muffins

A light crunch on the edges with a soft cheesecake center makes these Cream Cheese Carrot Cake Muffins irresistible!

Freshly shredded carrots give a warm pop of flavor to this sweet and rich cross between a cupcake, cheesecake and muffin.

Sweet cream cheese filling in the center of carrot cake muffins in a muffin tin next to fresh carrots

Carrot Cake Muffins with Cream Cheese Filling

Part muffin, part cupcake and mini cheesecake this recipe is easy to make and serve at brunch or for dessert. The delightful surprise in the center of the Cream Cheese Carrot Cake Muffins makes a unique treat that everyone in our family enjoys!

Our Farmhouse Carrot Bread might be the best quick bread we make. So when I came across this recipe for carrot cake muffins with cream cheese filling in an Amish cookbook I couldn’t resist trying it. Taking a similar batter with shredded carrots and adding a sweet cream cheese filling makes these muffins wonderful!

The carrot cake edge is like a cookie.  The cheesecake filling reminds me of the rich surprise in our Black Bottom Cupcakes. More carrot bread along the bottom and edges of the muffins makes a unique and delicious sweet treat.

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Carrot cake muffin with cream cheese filling on a white plate

We love cream cheese filled desserts from our Churro Cheesecake and Chocolate Chip Cheesecake Bars to our Cheesecake Cookie Bars.

Another similar treat is this 3 ingredient Pumpkin Carrot Cake from a box mix.

Tips & Tricks

  • A 14 1/2 ounce can of sliced carrots can be drained and used in place of the freshly shredded carrots
  • To add filling make a well in the center of the dough as best you can, but know that it is tricky to make each muffin uniform
  • Be careful not to overmix

How to Add the Filling

This muffin mixture is fairly thick and borderline dough more than batter. So I like to have a clean damp dishcloth close by to help make the process easier and to wipe up fingers or utensils as necessary.

Fill lined muffin tins about half full. Then use a spoon or clean fingers to make a well in one or two tins. The batter will not hold the well shape for very long is why I only do one or two at a time.

Use a different spoon to add a couple tablespoons of filling.

Then I take any extra filling that’s left and try to spread evenly over the top center of each muffin.

For a more even look not all of the filling is used, however we love the flavors and don’t want to waste any of it. So extra filling is always added to the top of the muffins in our house!

Fork of carrot cake muffin and cream cheese filling

Carrot Muffin with Cream Cheese Filling Recipe

Wash, peel and grate carrots. Gently stir carrots together with an egg and oil.

Mix up dry ingredients in a separate mixing bowl and slowly add to carrot mixture. Mix gently and take care not to over mix.

Using very soft cream cheese beat in another egg and sugar to make the cream cheese filling.

Line muffin tins and spoon or scoop batter into 12 tins. They will be about half full. Create a well in the center of each and spoon in cream cheese filling.

Muffin tin filled half full with carrot batter and adding cream cheese filling

Bake at 350°F for 20 to 25 minutes. These rich and sweet muffins taste great served warm with a glass of milk or at room temperature.

Store any extras in an air tight container in the refrigerator for up to 4 days.

Muffins can be double wrapped and frozen for up to 3 months.

More Delicious Muffin Recipes:

Banana Nut Mini Muffins can be made quickly in a blender or mixer and make perfect bites for little kids or adults.

Blueberry Banana Oatmeal Muffins have a wonderful flavor combination and a sweet cinnamon sugar mixture sprinkled on top that is delicious! Or try our Blueberry Coffee Cake which is like a muffin in cake form.

Bran and Raisin Molasses Muffins are old fashioned molasses muffins that have a sweet and rich taste while being packed full of fiber.  We love the unique flavors in these muffins!

Carrot cake muffin baked with cream cheese in the center

Cream Cheese Carrot Cake Muffins

Servings 12 muffins
Author: Jennifer
A crunchy edge with a soft cheesecake center makes these Cream Cheese Carrot Cake Muffins irresistible!
Prep Time 15 minutes
Cook Time 20 minutes
Total Time 35 minutes



  • 1 cup grated carrots
  • 1 egg
  • 1/2 cup vegetable oil
  • 1 3/4 cup all-purpose flour
  • 1 cup sugar
  • 1 1/4 teaspoon baking soda
  • 1/2 teaspoon salt
  • 1/2 teaspoon cinnamon
  • 1/8 teaspoon allspice
  • 1/8 teaspoon cloves
  • 1/8 teaspoon nutmeg


  • 8 ounces cream cheese softened
  • 1 egg
  • 1/4 cup sugar


  • Mix flour, sugar, baking soda, salt and spices in a small bowl.
  • Gently stir together carrots, 1 egg and oil. Then slowly add dry ingredients.
  • Fill muffin tins half full with batter. Using a spoon make wells in the center and spoon in filling. Bake at 350°F for 20 – 25 minutes.


Calories: 305kcalCarbohydrates: 37gProtein: 4gFat: 16gSaturated Fat: 11gTrans Fat: 1gCholesterol: 48mgSodium: 290mgPotassium: 91mgFiber: 1gSugar: 22gVitamin A: 2076IUVitamin C: 1mgCalcium: 30mgIron: 1mg

Nutritional Disclaimer

“Plowing Through Life” is not a dietitian or nutrition professional. Any nutritional information shared is an estimate and can vary greatly depending on specific products are used. If calorie count and other nutritional values are important to you, we recommend running the ingredients through an online nutritional calculator of your choice.

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