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Close up shot of cream cheese glazed carrot cake muffins

Carrot Cake Muffins with Cream Cheese Glaze

These Carrot Cake Muffins with Cream Cheese Glaze are on the healthier side - made with whole wheat pastry flour, almond flour, coconut oil, maple syrup, and Greek yogurt! They're super flavorful, and full of texture from grated carrots, shredded coconut, raisins, and chopped walnuts! And the best part - they're topped with a delicious cream cheese glaze!

Course Breakfast, Breakfast/Snack, Brunch, Dessert, Snack
Cuisine Breakfast, Healthier Baking
Keyword carrot cake muffins, carrot cake muffins with cream cheese glaze, easy carrot cake, healthier carrot cake muffins, healthy carrot cake, moist carrot cake recipe
Prep Time 25 minutes
Cook Time 20 minutes
Total Time 45 minutes
Servings 14 muffins
Author Molly | Spices in My DNA


For the muffins

  • 1 cup whole wheat pastry flour*
  • 1 cup almond flour*
  • 1 teaspoon baking powder
  • 1/2 teaspoon baking soda
  • 2 teaspoons cinnamon, plus extra for sprinkling
  • 1/2 teaspoon ground nutmeg
  • 1/2 teaspoon ground ginger
  • 1/2 teaspoon salt
  • 2 large eggs
  • 1/4 cup coconut oil, melted and slightly cooled
  • 1/2 cup pure maple syrup
  • 1/2 cup unsweetened vanilla almond milk*
  • 1/4 cup plain Greek yogurt
  • 2 teaspoons vanilla extract
  • 1 cup freshly grated carrots
  • 1/2 cup unsweetened shredded coconut
  • 1/2 cup raisins
  • 1/2 cup chopped walnuts

For the cream cheese glaze

  • 4 ounces cream cheese, softened to room temperature
  • 1/2 cup powdered sugar
  • 1/2 teaspoon vanilla extract
  • pinch of salt
  • 2-3 tablespoons unsweetened vanilla almond milk*


For the muffins

  1. Preheat oven to 425℉. Line a standard muffin tin with paper liners and spray liners with nonstick spray also. This recipe makes about 14 muffins, so if you have another tin, line it with two liners as well. Set aside.

  2. In a medium mixing bowl, combine the whole wheat pastry flour, almond meal, baking powder, baking soda, cinnamon, nutmeg, ginger, and salt. Whisk to combine and set aside.

  3. In another medium mixing bowl, whisk together the eggs, coconut oil, and maple syrup until combined. Add the almond milk, Greek yogurt, and vanilla and whisk again to combine. Add the carrots and stir to combine.

  4. Add the dry ingredients to the wet, folding with a rubber spatula until almost fully combined. Add the coconut, raisins, and walnuts, and stir until just evenly combined. (Don't overmix!)

  5. Fill muffin liners 3/4 full with batter. Bake for 5 minutes, then reduce oven temperature to 350℉ (leave the muffins in the oven!), and bake for an additional 18-20 minutes, or until set in the centers and a toothpick comes out clean. Let cool for 10 minutes in the tins, then remove and cool the rest of the way on a cooling rack.

  6. Once muffins are completely cool, spoon the cream cheese glaze over the muffins and sprinkle with extra cinnamon if desired!

For the cream cheese glaze

  1. Add cream cheese to a medium mixing bowl. Beat the cream cheese with electric beaters on medium-high speed until light and fluffy. Add the powdered sugar and beat until combined. Add the vanilla and salt and beat on medium-high until combined. Add the milk a tablespoon at a time, until desired consistency is reached and no lumps remain. Spoon over cooled muffins!

Recipe Notes

*This is the whole wheat pastry flour I use and love. You can also sub all purpose flour!
*This is the almond flour I use and love.
*You can sub any milk for the muffins! For the glaze, you can sub any milk also, or half and half/cream!