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Gluten free carrot cake muffins with cream cheese frosting on a cooling rack.
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Gluten Free Carrot Cake Muffins with Maple Cream Cheese Frosting (Paleo Option))

These healthy, naturally sweetened carrot cake muffins are gluten-free, grain-free, and are packed with carrots, but who cares, because THEY TASTE JUST LIKE CARROT CAKE! Oh, and did I mention that they get slathered with a Maple Cream Cheese Frosting?! (You'll only need a half batch of the frosting.) Best of all, the batter gets made entirely in the Vitamix or in a food processor. I encourage you to use an inexpensive scale when making these muffins—it’s not only easier (you won’t have to mess with a ton of measuring cups) but it’s also far more accurate. Be sure to check out my other muffin making tips above! These muffins are even better the next day, after all of the flavors have had time to meld.
Prep Time20 mins
Cook Time35 mins
Total Time55 mins
Course: Breakfast, Dessert
Cuisine: American
Keyword: carrot cake muffins, easy carrot cake muffins, healthy carrot cake recipe
Servings: 11 Muffins


  • Coconut oil or cooking spray for muffin tins
  • ½ cup (70 g) raisins
  • 3 medium carrots (220 g), peeled, trimmed and coarsely chopped
  • 3 large eggs
  • ¼ cup (80 g) maple syrup
  • ¼ cup coconut oil (48 g), melted and cooled slightly
  • 2 tablespoons unsweetened nut milk or regular milk
  • 2 teaspoons fresh lemon juice
  • 1 teaspoon grated fresh ginger
  • 1 teaspoon vanilla extract
  • 1 ¼ cup (125 g) finely ground almond flour
  • ¼ cup (25 g) coconut flour
  • ¼ cup (25 g) shredded unsweetened coconut
  • 2 teaspoons cinnamon
  • teaspoon freshly grated nutmeg
  • ¾ teaspoon baking soda
  • ½ teaspoon fine sea salt
  • cup (38 g) chopped walnuts or pecans, optional
  • ½ batch Maple Cream Cheese Frosting (optional), recipe link in header


  • Preheat the oven to 350˚F. Grease 11 muffin cups generously with coconut oil or cooking spray.
  • Cover the raisins with warm water and let sit.
  • Place the carrots in the Vitamix or food processor. If using the Vitamix, turn the machine on and gradually increase to medium speed (Variable 6 or 7), stirring with the tamper. Blend until the carrots are very finely chopped (it will only take a few seconds). If using the food processor, pulse the carrots until very finely chopped. Transfer to a bowl.
  • Place the container back on the base (no need to wash it—it’s ok if there are still some carrots around the edges and bottom), and add the eggs, maple syrup, coconut oil, milk, lemon juice, ginger and vanilla. Blend until smooth.
  • Sprinkle in the almond flour, coconut flour, coconut, cinnamon, nutmeg, baking soda and salt. Blend on low (Variable 2 or 3) or pulse (if using a food processor) until incorporated.
  • Drain the raisins, and add them to the batter along with the chopped carrots and nuts (if using). Blend on low (Variable 1), stirring with the tamper, or pulse if using a food processor, until just incorporated. Using a rubber spatula, scrape the sides and stir to fully incorporate all of the ingredients.
  • Scoop the mixture into the prepared muffin cups (an ice cream scoop works great for this). Bake 30-35 minutes, until the muffins are golden on top and a toothpick inserted in the center comes out clean. Cool in the tin for 5 minutes, then transfer the muffins to a cooling rack and let cool completely. 


Make it Ahead: The unfrosted muffins can be stored in an airtight container at room temperature for up to 3 days, or frozen for up to 3 months. Once frosted, the cupcakes can be refrigerated for up to 3 days.
  • When baking muffins it’s best to use a light colored pan, as dark pans can cause the bottoms and sides to darken too quickly.
  • I prefer to cook these muffins in oiled pans, but you can use paper liners if you prefer. Just be sure to let the muffins cool completely, otherwise they might stick to the liners.
  • I highly recommend investing in a kitchen scale, especially when working with gluten free flours. They’re not very expensive, and they make baking much easier (no measuring cups to wash!) and far more accurate (meaning better baked goods!).
  • I use Bob’s Red Mill almond flour and coconut flour, since they’re easy to find, affordable and reliably fresh.
  • If you don’t have a Vitamix you can use a Food Processor.
  • To take the muffins over-the-top, slather them with this Maple Cream Cheese Frosting (you'll only need a half batch). 
  • If it's an actual cake you're after, don't miss this Healthy Carrot Cake Recipe!