Cinnamon, nutmeg, ginger, and cloves spice up these Carrot Cake Muffins while a sweet cream cheese filling adds a creamy bit of cheesecake in each bite! Enjoy carrot cake for breakfast or any time of day with these easy muffins!

While there are all kinds of carrot cake variations around here, carrot cake in breakfast food form is definitely a favorite!

So, it’s no surprise that these Cream Cheese Filled Carrot Cake Muffins didn’t take long to disappear!

Packed with the warm, classic spices of cinnamon, nutmeg, and cloves, these muffins have all of the flavor of carrot cake. Just in a muffin form that you can enjoy any time of day!

Though the filling of these muffins isn’t as sweet and is more like a having a bit of cheesecake in each bite, the lightly sweetened cream cheese filling adds that creamy sweetness that you expect from the cream cheese frosting on a traditional carrot cake.

The combination of the spiced muffin and the sweet, creamy filling makes these muffins an irresistible option for enjoying carrot cake in a slightly healthier form.

Whether you want to have a couple for breakfast, a snack, or even dessert, these carrot cake muffins are sure to satisfy!

How to Make Carrot Cake Muffins with a Cream Cheese Filling

Start by preheating the oven to 375 degrees Fahrenheit. Line a muffin tin with cupcake liners or spray with non-stick cooking spray. 

In a large bowl, whisk together all-purpose flour, sugar, brown sugar, cinnamon, nutmeg, ginger, cloves, baking powder, baking soda, and salt. Set the bowl aside.

In a small to medium-sized bowl, whisk together the milk, unsweetened applesauce, coconut oil, eggs, and vanilla extract until combined.

Pour the wet ingredients into the dry ingredients. Stir the mixture together until just combined to keep the texture of the mixture tender. Fold in the grated carrots with a spatula.

In the bowl of a stand mixer, or in a medium bowl with a hand mixer, beat together the cream cheese, sugar, and vanilla extract until creamy and smooth.

Spoon one heaping Tablespoon of batter into each muffin cup, and spread batter so it evenly covers the bottom of the cup. 

Top with one heaping teaspoon of cream cheese mixture.

Cover cream cheese mixture with one heaping Tablespoon of muffin batter. Spread batter so that it completely covers the cream cheese. This will help keep the cream cheese filling from running out of the muffin while baking.

Repeat that process until the muffin batter and the cream cheese mixture are gone.

Bake muffins for 16-18 minutes, or until the tops are just starting to turn golden brown. The center should feel firm when tapped. Try not to over-bake the muffins as they dry out easily.

Remove the muffin tin to a wire rack to cool for 5 minutes before carefully removing the muffins from the tin to cool completely. If the muffins are too hot for you to touch after 5 minutes, wait until they are cool enough for you to handle before removing from the tin.

Store any leftover muffins in a covered container in the refrigerator.

Tips for Making Cream Cheese Filled Carrot Cake Muffins

• Depending on the size of your muffin tin cups, you will get around 12-14 muffins.
• Don’t skip lining the muffin tin with cupcake liners or spraying it with non-stick cooking spray. If the cream cheese filling leaks at all, the muffins will stick.
• These muffins work great for making the day before you need them. We actually liked the flavor of the muffins best the next day when all the flavors has a chance to blend.

Add additional flavors and textures with these optional add-ins:

• 1/2 Cup chopped pecans or walnuts
• 1/2 Cup raisins
• 1/2 Cup shredded coconut