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A cream cheese stuffed carrot cake muffin.

Carrot Cake Muffins with Cream Cheese Filling

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  • Author: Kelli Avila
  • Prep Time: 00:15
  • Cook Time: 00:20
  • Total Time: 35 minutes
  • Yield: 12 Muffins 1x
  • Category: Breakfast
  • Method: Baking


These perfectly spiced Carrot Cake Muffins are studded with shredded carrot, raisins and coconut and stuffed with a sweet cream cheese filling. This muffin recipe uses greek yogurt and light olive oil for added healthy fats (also making it perfectly moist) and is sweetened with maple syrup to make it much more acceptable to serve at breakfast. In addition, it has a nice level of warm spices with cinnamon, ginger, and nutmeg plus a little orange zest to round out the flavor. The muffin add-ins are carrots (of course), plumped raisins (see more on that below) and shredded coconut, but you can also swap in your favorite carrot cake additions.


Units Scale

For Cream Cheese Filling:

  • 4 ounces cream cheese, softened
  • 1/2 cup powdered sugar
  • 1/2 teaspoon vanilla extract

For Carrot Cake Muffins:

  • 2 large eggs
  • 1/2 cup (130 grams) full-fat Greek yogurt
  • 1/2 cup pure maple syrup
  • 1/4 cup light olive oil
  • 1 teaspoon vanilla extract
  • 1 tablespoon orange zest
  • 2 teaspoons baking powder
  • 1-3/4 cup (210 grams) all-purpose flour
  • 1-1/2 teaspoons ground cinnamon
  • 1/2 teaspoon ground ginger
  • 1/4 teaspoon ground nutmeg
  • 1 cup shredded carrots (see note)
  • 1/2 cup plump raisins (see note)
  • 1/4 cup finely shredded unsweetened coconut


  1. Preheat the oven to 350ºF and place parchment paper liners in a 12 cup muffin tin.
  2. Add softened cream cheese, powdered sugar, and vanilla extract to a bowl and mash the mixture with a sturdy spoon. Once the sugar has been combined with the cream cheese, switch over to a whisk and vigorously whisk until it’s smooth. Set aside.
  3. Add the eggs, greek yogurt, maple syrup, light olive oil, vanilla extract, orange zest and baking powder to a large bowl and whisk until well combined.
  4. Add in the flour, cinnamon, ginger, and nutmeg and mix until barely combined.
  5. Fold in the shredded carrots, raisins and coconut.
  6. Place two heaping tablespoons of batter in each muffin tin (or one scoop with a size "30" portion scooper). Use a spoon to spread the batter flat. It does not need to be perfect. Then add 1 heaping tablespoon of cream cheese frosting, and use a spoon to spread out the frosting. Repeat with 2 heaping tablespoons of muffin batter, spreading it out to cover the frosting. Bang the muffin tin on a hard surface once or twice to help the muffin batter settle.
  7. Bake in the preheated oven for 18-20 minutes, or until the muffin tops are matte in appearance and firm to the touch.
  8. Let the muffins cool slightly before serving.


Some people like finely grated carrots in their carrot cake, and some prefer more coarse. Feel free to shred them to your liking.

Rehydrating raisins before adding them to the muffin batter results in a better muffin. You're met with a moist and soft raisin instead of a hard and dry one when you bite into it. To rehydrate raisins, place them in a heat-safe bowl and cover them with very hot or boiling water. They'll be plumped within minutes. Drain the raisins when ready to add to the batter.