Healthier Gluten Free Carrot Cake Cupcakes

Name: Gluten Free Carrot Cake Cupcakes with Cream Cheese Frosting
Prep time: 15 min
Cook time: 22 min
Total time: 37 min
Ingredients: 1 1/2 cups gluten free flour blend (* see note); 1/2 cup almond milk (* see note); 1 1/2 cups shredded carrot; 1 teaspoon baking powder; 1/2 teaspoon baking soda; 1/8 teaspoon sea salt; 1/4 teaspoon ground allspice; 1/2 teaspoon ground nutmeg; 1 1/2 teaspoon ground cinnamon; 1 1/4 cups coconut sugar; 3 large eggs; 1/4 cup coconut oil (melted); 3 ounces apple sauce (unsweetened); 3 tablespoons chia seeds; 8 ounces softened cream cheese (* see note); 1/4 cup softened butter; 1 teaspoon pure vanilla extract; 2 cups powdered sugar

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If you love carrot cake, you are going to love my recipe for gluten free carrot cake cupcakes! These decadent carrot cupcakes are topped with a homemade cream cheese frosting that tastes just as good as your grandma's!

Sprinkling shredded coconut over a cupcake.

Jump to:

Why These Cupcakes Are Great:
How To Shred Carrots For Baking:
Ingredient Notes:
Healthy Additions:
How To Make Carrot Cake Cupcakes:
Expert Tips and Recipe FAQ:
More Delicious Gluten Free Cupcake Recipes:
📖 Recipe
Fearless Dining
💬 Comments

This is a treasured recipe that I both converted to gluten free and made healthier. It is my Grandma's homemade carrot cake. I always remembered her carrot cake was made from scratch, and it was so moist and delicious! I knew I wanted to recreate it, but a better, less guilty version.

Carrot cake cupcakes are a type of cupcake that you can make all year long. I use real, whole-food ingredients that are available in any local grocery store. All you need to do is follow the simple steps, and you will be enjoying homemade cupcakes in no time!

These cupcakes are the real deal and taste as if they came from a bakery! For the best cupcake recipes, check out my Gluten Free Cupcakes resource guide!!

Why These Cupcakes Are Great:

These cupcakes are "healthier" cupcakes and have lots of carrots, chia seeds, and no-refined sugars. They are one of my kids' favorite recipes.
They are topped with a thick and creamy cream cheese frosting that tastes so good on these carrot cupcakes!!
You can freeze these cupcakes so you have them on hand anytime.

If you love cupcakes as much as I do, here are a couple of my favorite cupcake recipes on Fearless Dining for you to also try: Gluten Free Lemon Cupcakes with a Lemonade Drizzle and these Gluten Free Chocolate Cupcakes.

How To Shred Carrots For Baking:

My favorite way to shred carrots for baking is in my food processor. This is quick and easy. You can also use a grater. A grater lets you choose between several sizes so you always have the best size for your recipe.

Once you have the shredded carrots, I use a paper towel and squeeze the carrot shreds to get the extra moisture out. This will help prevent soggy cupcakes.

Top Pick

King Arthur, Measure for Measure Flour 3 lbs

This is one of my favorite gluten-free flour blends for cookies, cakes, pie crust, biscuits, and muffins! (Do not use this flour blend for yeast recipes.)

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Ingredient Notes:

Photos of the carrot cake cupcakes ingredients.

Gluten free flour blend - I tested this recipe using Bob's Red Mill 1 to 1 Gluten Free Flour Blend, Pillsbury Gluten Free Flour Blend and King Arthur's Measure for Measure Gluten Free Blend flour mixtures. That doesn't mean others will not work, I just have not tested other flours, and I can not guarantee the recipe will work if you use other mixes. That doesn't mean others will not work. I just have not tested other flours.
Xanthan gum - If your blend doesn't contain it, you will need to add xanthan gum or guar gum. This is important, so your cupcakes hold together.
Non-dairy milk - Other dairy-free kinds of milk will work but I do not recommend canned coconut milk. I like to use almond milk for baking.
Coconut sugar - If you prefer, you can use brown sugar.
Applesauce - Use unsweetened if you see that in your grocery store.
Cream Cheese - Most cream cheese is gluten-free, but check Is Cream Cheese Gluten Free to be sure.

This gluten free carrot cake cupcakes recipe is made without pineapple. If you like pineapple, you can substitute crushed pineapple instead of the applesauce in this recipe. You may also love these Gluten Free Coconut Cupcakes.

Healthy Additions:

Add 2 tablespoons of ground flaxseed meal.
Add 1-2 tablespoons of chia seeds. (*Note this will make your cupcakes a bit dense as these make the cupcakes hold more moisture.)
Add more almond flour (1 cup gluten free flour blended with 1 cup almond flour). You may need to reduce the liquids to ⅔ cup almond milk and ¼ cup coconut oil.
Add nuts like walnuts or pecans.

You can also add different seasonings to this recipe. I have made this gluten free carrot cake cupcake recipe with added cardamom. (I omitted the nutmeg and allspice when I added cardamom.)

If you love coconut that tops this cupcake, you will want to also try my Gluten Free Coconut Cupcakes recipe!

My Pick

REGILLER Stainless Steel Mixing Bowls (Set of 5), Non Slip Silicone Bottom Nesting Storage Bowls

I always recommend mixing any batter by hand. That means don't use a stand mixer. Mixing by hand means your baked goods will turn out light and fluffy. Mixing by hand can be a pain, but using these bowls with rubber bottoms makes it easier. They don't slide all over the counter while you mix your wet and dry ingredients together.

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How To Make Carrot Cake Cupcakes:

The first step is to move your oven rack to a middle position. Set the temperature of the oven to 350º F to preheat your oven.

Step 1: Add the gluten free flour, baking powder, baking soda, spices, and sea salt to a large mixing bowl. Whisk to blend the dry ingredients together.

The best way to be sure your flour is measured accurately I recommend using either the spoon method or leveling method. I didn't use a kitchen scale because every gluten free flour blend has a different weight.

Spoon Method: You can also use a spoon to fill the measuring cup. Use a knife to level along the top to remove the extra flour.

Leveling Method: Put the measuring scoop into the flour and fill. Do not pack the flour. Use a knife to scrape along the top to remove the extra flour.

Step 2: In a smaller bowl, add your eggs, coconut sugar, apple sauce, melted coconut oil, and shredded carrots. Mix well with a whisk.

Step 3: Pour the wet ingredients into the dry ingredients and mix until "just barely mixed." Do not over-mix your batter, or your cupcakes will turn out dense.

After mixing the cupcake ingredients, you will have a semi-thick gluten free carrot cake batter, like in the picture. I do not recommend using a standing mixer for best results because it tends to overmix your batter, making your cupcakes denser.

Step 4: This is what your cupcake batter should look like after it is mixed. I used a slightly thicker size on my grater so the carrot chunks are a little bigger.

Step 5: Line a muffin tin with parchment paper cupcake liners and fill each ¾ full of batter. You can use a large cookie scoop to drop the batter into the cupcake sections or spoon the batter in with a large spoon.

Optional: Let the batter sit for 10-15 minutes. This can eliminate some of the grittiness that some gluten free flour blends can have.

Step 6: Bake your gluten free carrot cake cupcakes at 350º F for 20-25 minutes. Remove from the oven and cool before frosting.

Note: You can also use this batter to make a sheet cake, layer cake, or a gluten free carrot roll cake.

How To Make The Cream Cheese Frosting:

Step 7: Make the frosting by adding the room-temperature cream cheese, powdered sugar, vanilla extract, and unsalted butter (softened) to a mixer.

Mix on low speed and gradually increase the speed to high until the frosting is nice and fluffy. The cream cheese helps make this frosting the creamiest!

Step 8: Frost your cupcakes any way you like. Add the cream cheese frosting to a pastry bag, choose a medium-sized star tip, and squeeze the frosting onto each cupcake.

Sprinkle the cupcakes with unsweetened shredded coconut and enjoy! You can also have fun decorating the cupcakes for Easter by tinting your coconut to a green color and topping the cupcakes with jelly beans.

If you want to try another incredible light and fluffy cupcake recipe, my Gluten Free Pumpkin Cupcakes are out of this world good!

Expert Tips and Recipe FAQ:

For more easy gluten free baking tips, read my guide to the best flours for gluten free baking.

How long do you bake carrot cake cupcakes?

Place paper liners into a muffin tin and fill each cup with the cupcake batter. Bake at 350º F for 20-25 minutes until done. Remove the cupcakes to a wire cooling rack.

How do you know when your cupcakes are finished baking?

To test for doneness, insert a toothpick into the center of a cupcake. If the toothpick comes out clean, it is done baking. If you see batter or crumbs, the cupcakes need to be baked longer.

Can you make this dairy-free?

You can definitely make this gluten free cupcake recipe dairy-free. You can use dairy-free cream cheese like Daiya or Kite Hill to make the frosting.

Can you make this cupcake recipe nut-free?

This recipe is easy to make nut-free by using different non-dairy milk.

How long will these cupcakes keep fresh?

These cupcakes will keep for up to 3 days in an air-tight container or in the freezer for up to 4 months. They may need to be microwaved to soften them after storing them in the refrigerator.

Can you store these gluten free carrot cake cupcakes in the fridge?

You can easily store these gluten free carrot cupcakes in the fridge. It is actually recommended so they keep fresh for longer.