Gluten Free Carrot Cake Cupcakes

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Homemade gluten free Carrot Cake Cupcakes are loaded with fresh carrots and feature warm spices, crunchy pecans, and a hint of brown sugar. They are so moist and delicious that they are sure to disappear just as quickly as you made them. Frost them with a gorgeously fluffy cream cheese frosting for a homey and always welcome classic treat!

A side view of a cream cheese frosting-topped carrot cake cupcake.

Why This Is The Best Gluten Free Carrot Cake Cupcakes Recipe

If you love carrot cake – like me! – you’re going to love it turned into carrot cake cupcakes. These gluten free carrot cake cupcakes have a rich molasses note from brown sugar in the batter and the fresh, sweet carrots are nicely offset by crunchy toasted pecans. The tangy cream cheese frosting is the classic and perfect finishing touch.

  • Cuisine Inspiration: American
  • Primary Cooking Method: Oven
  • Dietary Info: Gluten-free, Dairy-free option
  • Skill Level: Easy

Everything you love about carrot cake in a handheld cupcake? Yes, please! Here’s why you’ll love this recipe:

  • The best carrot cake cupcakes recipe. I happen to think this is the best carrot cake cupcakes recipe you’ll find. It’s so simple to whip up and you can quickly grab all of the ingredients at your grocery store. And they are moist and tender. In fact, they are so good that nobody will believe they are gluten free.
  • Gluten-Free. This is a gluten-free cupcake recipe and it relies on a 1:1 all-purpose gluten free flour blend to give the cupcakes structure without the fuss of multiple flours and starches. The rest of the ingredients you’ll need are naturally gluten free.
  • Flavorful and rich. Packed with cozy spices like cinnamon, ginger, nutmeg, and allspice plus a hint of natural sweetness from applesauce, the flavors going on in these gluten free carrot cake cupcakes will wrap around you like a warm blanket.
A carrot cake cupcake half shows its interior.

Carrot Cupcakes Ingredients

Here’s an overview of what you’ll need to make gluten free carrot cake cupcakes. The full ingredient amounts are included in the recipe card at the end of this post.

For the Cupcakes

  • Gluten Free Flour: I recommend King Arthur Flour Measure for Measure.
  • Leavening Agents: Baking powder and baking soda.
  • Ground Spices: Cinnamon, nutmeg, ginger, and allspice.
  • Salt
  • Vegetable Oil: Or you can use another neutral-flavored oil.
  • Granulated Sugar
  • Brown Sugar: You can use light or dark brown sugar.
  • Eggs: Use large eggs.
  • Vanilla Extract: Pure vanilla extract will give the best flavor!
  • Applesauce: Use unsweetened applesauce,
  • Carrots
  • Pecans: For a nice bit of crunch.
Ingredients for Gluten Free Carrot Cake Cupcakes.

For the Frosting

If you need to make dairy-free cupcakes, just use the vegan versions of the cream cheese and butter.

  • Cream Cheese: Use block cream cheese rather than whipped cream cheese.
  • Butter: Use unsalted butter.
  • Powdered Sugar: Make sure to sift the sugar before using it.
  • Vanilla Extract: If possible, use clear vanilla extract so it doesn’t affect the color of the frosting. 
  • Pecans: Optional, for a garnish.
Ingredients to make the frosting for Gluten Free Carrot Cake Cupcakes.

How to Make Gluten Free Carrot Cake Cupcakes

This recipe is adapted from my Gluten Free Carrot Cake recipe, and it could hardly be simpler to make. The detailed instructions are in the recipe card lower down.

  • Prepare. Preheat the oven and line a 12-cup muffin pan.
  • Sift. Using a mesh strainer, sift the dry ingredients together.
  • Mix. Beat the oil, sugar, and brown sugar together.
  • Add eggs. Beat in the vanilla and the eggs.
  • Combine. Now beat in the flour mix.
  • Add applesauce. Beat in the applesauce until smooth.
  • Finish. Fold in the carrots and pecans.
  • Bake. Divide the batter between the cupcake wells and bake for 20-25 minutes.
  • Cool. Remove cupcakes from the oven, cool in the pan, then cool on a wire rack.
  • Make frosting. Beat the cream cheese and butter together, then add the powdered sugar and vanilla.
  • Assemble. Pipe the frosting onto each cupcake. Garnish with a dusting of cinnamon or some toasted pecans, if desired.

Tips for the Best Carrot Cupcakes

Here are a few gluten free baking tips that can help your carrot cake cupcakes turn out beautifully:
  • Measure the flour properly. Ideally, you will use a kitchen scale to weigh your flour – this is a must in gluten free baking! If you don’t have a scale, the next best method is the spoon-and-sweep method. Rather than scooping the flour out of the bag, spoon the flour into your measuring cup, then use the back of a knife to level it off.
  • Use room temperature ingredients. This is especially important when you make the frosting. Cream cheese is incorporated much better into frosting or batter when it’s softened up a bit at room temperature. Butter should also be softened to room temperature for the best texture in frosting.
  • Sift the powdered sugar. Sifting powdered sugar is an essential step when making any type of frosting! This will eliminate any lumps in the frosting.
  • Grate the carrots with a food processor. This is a simple trick that will help you make fresh grated carrots in seconds! Use the grater plate or blade on your food processor and skip the box grater.
  • Add cupcake liners. To ensure the easiest release from the cupcake pan, use cupcake liners to hold the batter. If you don’t have liners, make sure to thoroughly grease and use gluten-free flour to dust the cupcake tin before pouring in the batter.
  • Make it dairy-free. If you need to make this into a dairy-free recipe, no problem. Swap the butter for your favorite non-dairy butter and use a non-dairy cream cheese for the cream cheese.
Four frosted carrot cake cupcakes on a glass cake stand.

Proper Storage

Here’s how to store homemade carrot cake cupcakes:

  • Fridge – Place leftover gluten free carrot cake cupcakes in an airtight container or tightly cover them with foil and store them in the fridge for up to 5 days. Let the cupcakes sit at room temperature for a short while before serving them for the best texture.
  • Freezer – You can freeze carrot cake cupcakes in an airtight, freezer-safe container for up to 3 months. Make sure to thaw the cupcakes thoroughly in the fridge before serving them.
A glass cake stand holds pecan-topped carrot cake cupcakes.
Carrot cake cupcakes frosted with cream cheese frosting are garnished with pecans.
5 from 1 vote

Gluten Free Carrot Cake Cupcakes

Homemade gluten free Carrot Cake Cupcakes are loaded with fresh carrots and feature warm spices, crunchy pecans, and a hint of brown sugar. They are so moist and delicious that they are sure to disappear just as quickly as you made them. Frost them with a gorgeously fluffy cream cheese frosting for a homey and always welcome classic treat!
Prep: 20 minutes
Cook: 25 minutes
Total: 45 minutes
Servings: 12 cupcakes


For the cupcakes

  • 1 ¼ cups 1-to-1 gluten free flour, 150 grams (recommended: King Arthur Flour Measure for Measure)
  • 1 teaspoon baking powder
  • ½ teaspoon baking soda
  • 1 teaspoon cinnamon
  • teaspoon nutmeg
  • ¼ teaspoon ginger
  • ¼ teaspoon allspice
  • ¼ teaspoon salt
  • ¼ cup vegetable oil
  • ½ cup granulated sugar
  • cup light brown sugar, lightly packed
  • 2 large eggs
  • ½ teaspoon vanilla extract
  • ¼ cup applesauce
  • 1 cup shredded carrots
  • cup chopped pecans (toasted, if desired)

For the frosting

  • 8 ounces cream cheese, at room temperature (non-dairy, if needed)
  • ½ cup unsalted butter, at room temperature (vegan butter, if needed)
  • 3-4 cups powdered sugar, sifted
  • 1 Tablespoon vanilla extract (clear is recommended, but not necessary)
  • Pecans, whole or chopped (toasted, if desired) and cinnamon for decoration, optional


For the cupcakes:

  • Preheat the oven to 350°F. Line a 12-cup muffin pan with cupcake liners.
  • Sift the flour, baking powder, baking soda, cinnamon, nutmeg, ginger, allspice, and salt together into a medium bowl.
  • Add the oil, sugar, and brown sugar to a large bowl. Beat with a hand mixer on medium speed for 2-3 minutes. Scrape down the bowl.
  • Beat in the vanilla, followed by the eggs, one at a time, mixing for 60 seconds between each egg.
  • Turn the mixer to low speed and add the flour mixture. Mix until just combined, then blend in the applesauce.
  • Add the carrots and pecans and fold them in with a spatula by hand until they are evenly distributed.
  • Fill the cupcake liners approximately 2⁄3 full and bake for 20-25 minutes or until the top springs back when gently pressed.
  • Remove from the oven and cool in the pan for 10 minutes, then remove from the pan and transfer to a wire rack. Cool completely before piping or spreading the frosting generously on each cupcake and decorating with a dusting of cinnamon and pecans, if desired.

For the frosting:

  • Combine cream cheese and butter in a large bowl and beat with a hand mixer or stand mixer 2-3 minutes until smooth and creamy. Scrape down the bowl.
  • Add the vanilla and 3 cups of the powdered sugar. Start the mixer on low speed. Stir until the sugar is all incorporated. The mixture will resemble a thick paste.
  • Turn the mixer to high speed and beat for 5 minutes, until the frosting is fluffy and lighter in color. Add additional powdered sugar if needed to achieve the desired consistency.
Nutrition Facts
Gluten Free Carrot Cake Cupcakes
Amount Per Serving
Calories 430 Calories from Fat 198
% Daily Value*
Fat 22g34%
Saturated Fat 10g50%
Trans Fat 0.3g
Polyunsaturated Fat 4g
Monounsaturated Fat 6g
Cholesterol 67mg22%
Sodium 127mg5%
Potassium 133mg4%
Carbohydrates 57g19%
Fiber 2g8%
Sugar 46g51%
Protein 4g8%
Vitamin A 2316IU46%
Vitamin C 1mg1%
Calcium 61mg6%
Iron 1mg6%
* Percent Daily Values are based on a 2000 calorie diet.
Disclaimers: Please discuss your individual dietary needs (i.e. gluten free) with a physician. Even when not specified, be sure to verify all ingredients are gluten free, if needed, by reading labels on all packaging and/or confirming with the manufacturer this varies by brand and can change at any time. Nutrition information shown is an estimate and not guaranteed to be accurate.


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