Carrot cake muffins cream cheese filling
Sarah Biren
Sarah Biren
June 23, 2020 ·  4 min read

Carrot Cake Muffins Recipe With Cheesecake Fillings (GF, Vegan, Paleo Option)

Carrot cake and cream cheese frosting is a true match made in heaven, especially when baked into a delicious morning treat. After all, what are muffins but cupcakes we eat for breakfast? These carrot cake muffins are moist and fluffy, rich in carrot-cinnamon goodness, and filled with sweet and creamy cheesecake.

It’s enough of an incentive for anyone to get out of bed, although these muffins are perfect for any time of day. The streusel on top adds an extra kick of sugar and spice and the glaze ties in all of the sweet flavors together. 

This recipe may not be ideal for every day eating, but they are the best for scrumptious, occasional treats. We’ve provided an alternative version of this recipe for those who would prefer a healthier alternative, which is also gluten-free, dairy-free, paleo, and vegan-friendly. 

Whichever version you choose is sure to brighten up your mornings! 

Carrot Cake Muffins with Cheesecake Fillings 


For Carrot Cake Muffins: 

  • 2 1/4 cups all-purpose flour 
  • 1/2 cup granulated sugar 
  • 1/4 cup light brown sugar (firmly packed) 
  • 1 1/2 teaspoons baking powder 
  • 1/4 teaspoon baking soda 
  • 1 1/2 teaspoons ground cinnamon 
  • 3/4 teaspoon ground ginger 
  • 3/4 teaspoon salt 
  • 2 large eggs 
  • 3/4 cup water 
  • 1/3 cup avocado oil 
  • 1 cup grated carrots (about 2–3 medium carrots) 

For the cream cheese filling: 

  • 10-ounce cream cheese-softened 
  • 1/4 cup+1 Tablespoon sugar 
  • 1/2 teaspoon vanilla 

For the streusel topping: 

  • 1 cup all-purpose flour 
  • 2/3 cup granulated sugar 
  • 1 /2 cup unsalted butter-melted 
  • 1 teaspoon cinnamon 
  • 1/4 teaspoon salt 

For the glaze: 

  • 1 tsp milk 
  • 1/4 cup powdered sugar 


  1. Preheat the oven to 400°F. 
  2. Place cupcake liners in a standard cupcake pan and set aside. 
  3. For the streusel topping: In a medium bowl stir together 1 cup all-purpose flour, 2/3 cup granulated sugar, 1 teaspoon cinnamon and 1/4 teaspoon salt, add 1 /2 cup melted unsalted butter melted and stir it with a fork until crumbly. Set aside. 
  4. For the cream cheese filling: Beat together the cream cheese, vanilla and sugar until smooth. Set aside. 
  5. For the muffins: In a large bowl, whisk together all dry ingredients listed for the muffins. 
  6. In a small bowl, whisk together the eggs, water, and oil. 
  7. Stir the egg mixture into dry ingredients. 
  8. Fold in the grated carrots and stir well to combine. 
  9. Drop about 1 ½ to 2 tbsp of the batter into each cup and spread to cover the bottom, then place 1 heaping tablespoon of the cream cheese filling in each. Cover the filling over with more batter to fill the cups 3/4 full. 
  10. Sprinkle the cupcakes with streusel topping and bake for about 20 minutes, until the toothpick inserted in the cake (not cream cheese filling) comes out clean. 
  11. Remove the muffins from the oven, let them cool for 10 minutes in the pan, then transfer to a cooling rack. 
  12. For the glaze: Stir 1 tablespoon milk with 1/4 cup powdered sugar until mixed well, and drizzle over the cooled muffins before serving. 

Read: Carrot Cake Sandwich Cookies With Cream Cheese Frosting (Vegan and Gluten-free Options)

Carrot Cake Muffins with ‘Cream Cheeze’ Filling – gluten-free, dairy-free, paleo, and vegan-friendly


For the filling: 

  • 6 ounces (170 grams) vegan cream cheese 
  • 3 tablespoons coconut sugar*  
  • 1/2 teaspoon vanilla extract 
  • pinch of salt 

For the carrot cake muffins: 

  • 1 1/4 cups (125 grams) blanched almond flour 
  • 2 tablespoons (16 grams) coconut flour, sifted if lumpy 
  • 1/2 teaspoon baking soda 
  • 1/8 teaspoon salt 
  • 1 1/2 teaspoons ground cinnamon 
  • 1/2 teaspoon ground ginger 
  • 1/4 teaspoon ground nutmeg 
  • 2 large eggs, room temperature 
  • 1/3 cup (75 grams) coconut oil, melted 
  • 1/3 cup (106 grams) honey** 
  • 2 teaspoons vanilla extract 
  • 1/2 cup (50 grams) grated carrots 

* If you’re looking to reduce sugar and calories, try a 1:1 Golden Monk Fruit Sugar instead of coconut sugar.
** Honey can be hard to substitute, but low calorie, natural alternatives do exist. If you can’t have honey or are looking to cut the sugar or calories, you can try something like this as a 1:1 substitute.


  1. Preheat the oven to 350°F (175°C). Line a muffin tin with 10 muffin liners. 
  2. For the filling: In a medium bowl, beat all filling ingredients with an electric hand mixer at medium speed until light and fluffy. Set aside. 
  3. For the muffins: In a medium mixing bowl, mix the dry ingredients (almond flour through nutmeg). Set aside. 
  4. In a large mixing bowl, mix together the eggs, oil, honey, and vanilla extract. 
  5. Add the dry mixture to the wet mixture, stirring until combined, and then gently fold in the grated carrots. 
  6. Pour a little batter into each cup, about 1/5 or 1/4 full. Add about 1 tablespoon of cheesecake filling and cover with the remaining muffin batter. 
  7. Bake for 20 minutes or until a toothpick inserted in the side of a muffin (not the center with the filling) comes out clean. 
  8. Let the muffins cool for 5 minutes in the pan and then remove to a wire rack to cool completely. Refrigerate in an airtight container for up to 3 days. 

Optional: Add a streusel topping just before baking the muffins. 

Simply mix: 

  • 1 tablespoon (14 grams) coconut oil, melted 
  • 1 tablespoon maple syrup 
  • 1/4 teaspoon ground cinnamon 
  • pinch of salt 
  • 1/3 cup (33 grams) almond flour 
  • 1/2 cup (55 grams) finely chopped walnuts 

Keep Reading: Lavender Cupcakes with Honey Cream Cheese Frosting (Gluten-free and Vegan Options)