Gluten Free Carrot Cake Cupcakes

Homemade Gluten Free Carrot Cake Cupcakes are loaded with fresh carrots and feature warm spices, crunchy pecans, and the caramelized flavor 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 fluffy cream cheese frosting for a classic treat that’s welcome for any holiday or occasion!

Delicious Details
- Cuisine Inspiration: American
- Primary Cooking Method: Oven
- Dietary Info: Gluten-free, Dairy-free option
- Skill Level: Easy
If you love carrot cake – like me – you’re going to love it turned into carrot cake cupcakes. I have been known to eat nearly an entire carrot cake myself back many years ago at my work baby shower. So carrot cake in cupcake form is the perfect way for me to get the satisfaction of finishing my own portion of carrot cake without going back for another sliver… and another sliver… and another sliver…
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.
The Ultimate Gluten Free Carrot Cake Cupcakes Recipe
Everything you love about carrot cake in a handheld cupcake? Yes, please! Here’s why you’ll love this recipe:
- A fuss-free carrot cake cupcake recipe. I happen to think this is the only recipe for gluten free carrot cake cupcakes you’ll even need. It’s so simple to whip up, and you can easily find all of the ingredients in your fridge or pantry, and maybe a quick run to any grocery store – nothing fancy to look for! It it relies on a 1:1 all-purpose gluten free flour blend instead of multiple flours and starches.
- The texture you love. They are so moist, tender, and tasty that nobody will believe they are 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.

Recipe 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, such as avocado 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. You can lightly toast them to develop the nutty flavor.

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. Again, I recommend lightly toasting them.

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 Success
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.
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.

More Gluten Free Cupcake Recipes

Gluten Free Carrot Cake Cupcakes
Ingredients
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
- ¼ teaspoon salt
- 1 teaspoon cinnamon
- ¼ teaspoon ginger
- ¼ teaspoon allspice
- ⅛ teaspoon nutmeg
- ¼ cup vegetable oil
- ½ cup granulated sugar
- ⅓ cup light brown sugar , lightly packed
- ½ teaspoon vanilla extract
- 2 large eggs
- ¼ cup unsweetened applesauce
- 1 cup shredded carrots
- ⅓ 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)
- 1 Tablespoon vanilla extract (clear is recommended, but not necessary)
- 4 cups powdered sugar , sifted
- whole or chopped pecans (toasted, if desired) and cinnamon for decoration, optional
Instructions
For the cupcakes:
- Preheat the oven to 350°F. Line a 12-cup muffin pan with cupcake liners.
- Sift 1 ¼ cups 1-to-1 gluten free flour (150 grams), 1 teaspoon baking powder, ½ teaspoon baking soda, ¼ teaspoon salt, 1 teaspoon cinnamon, ¼ teaspoon ginger, ¼ teaspoon allspice, and ⅛ teaspoon nutmeg together into a medium bowl.
- Add ¼ cup vegetable oil, ½ cup granulated sugar, and ⅓ cup light brown sugar to a large bowl. Beat with a hand mixer on medium speed for 2-3 minutes. Scrape down the bowl.
- Beat in ½ teaspoon vanilla extract, followed by 2 large 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 ¼ cup unsweetened applesauce.
- Add 1 cup shredded carrots and ⅓ cup chopped 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 whole or chopped pecans, if desired.
For the frosting:
- Combine8 ounces cream cheese and ½ cup unsalted 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 1 Tablespoon vanilla extract and 3 cups 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 up to an additional 1 cups powdered sugar a little at a time, if needed to achieve the desired consistency.




