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!
This post may contain affiliate links. Please read our Disclosure Policy.
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 remember her carrot cake being made from scratch; 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 you can make all year. I use real, whole-food ingredients that are available in any local grocery store. Follow the simple steps, and you will be enjoying homemade cupcakes in no time!
For the best cupcake recipes, check out my Gluten Free Cupcakes resource guide!!
Why we love making this gluten-free carrot cupcake recipe:
- These cupcakes have lots of carrots, chia seeds, and no refined sugars. They are one of my kids’ favorite recipes. These cupcakes are the real deal and taste as if they came from a bakery!
- They are topped with a thick, 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.
These cupcakes were INCREDIBLE! My fiancé loved them so much and so did my roommate. I love the chia seeds and I added the flaxseed in as well from your substitution list. I can’t wait to try more of your recipes. Thank you so much for the sweet treat!
missy, blog comment
Allergen Information:
These homemade carrot cupcakes are gluten-free, dairy-free, nut-free, oat-free, soy-free, and refined sugar-free.
You can make the frosting in this recipe dairy-free by using dairy-free cream cheese like Daiya or Kite Hill.
Ingredient Notes:
For the full list of ingredients and amounts, please go to the recipe card below.
- 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 must add xanthan gum or guar gum. This is important so your cupcakes hold together.
- Baking Powder – Use aluminum-free baking powder.
- 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 with applesauce in this recipe. You may also love these Gluten Free Coconut Cupcakes.
Try these wholesome mix-ins:
- 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 2/3 cup almond milk and 1/4 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 Cupcake recipe!
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.
Step-By-Step Photos and Directions:
The first step is to move your oven rack to the middle position. Then, set the oven temperature to 350º F to preheat it.
Email This Recipe To Me!
I will email this recipe to you, so you can come back to it later!
Step 1: Add the gluten free flour, baking powder, baking soda, spices, and sea salt to a large
The best way to be sure your flour is measured accurately. I recommend using either the spoon method or the 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: Fill the measuring scoop with flour, but do not pack it. 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.
📢 Sandi says: Every gluten-free flour blend has a different starch-to-grain ratio. The brand of gluten-free flour you use will affect the moisture of the batter. If your cake batter is too runny, add more flour, and if it is too thick, add more liquids.
Read Why Gluten-Free Flour Blends Vary to learn more about this.
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 3/4 full of batter. You can use a large
Optional: Let the batter sit for 10-15 minutes. This can eliminate some of the grittiness some gluten free flour blends can have.
Step 6: Bake the gluten-free carrot cupcakes at 350º F for 20-25 minutes. Remove from the oven. To test for doneness, insert a toothpick into the center of a cupcake. If it comes out clean, they are finished baking. If you see crumbs or batter, they need to bake a little longer.
Step 7: Place the cupcakes onto a cooling rack and allow them to cool fully before frosting.
Note: You can also use this batter to make a sheet, layer, or 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 the ingredients 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 the coconut green and topping them 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!
Frequently Asked Questions:
For more easy gluten free baking tips, read my guide to the best flours for gluten free 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 must be baked longer.
These cupcakes will keep fresh for up to 3 days in an airtight container or in the freezer for up to 4 months. After storing them in the refrigerator, they may need to be microwaved to soften.
You can easily store these gluten free carrot cupcakes in the fridge. It is actually recommended that they stay fresh for longer.
More Delicious Gluten Free Cupcake Recipes:
- Filled cupcakes like this Gluten Free Lemon Curd Filled Cupcakes recipe is all the rage!
- Intense mocha flavors in these Gluten Free Mocha Cupcakes with Mocha Buttercream make them hard to resist!
- These Gluten Free Vanilla Cupcakes make the best birthday cupcakes!
Love This Recipe?
If you made and enjoyed this recipe, I would be incredibly grateful if you could leave a comment below. Please include which flour blend you used. This will help others know this recipe is delicious. Thank you!
Gluten Free Carrot Cake Cupcakes with Cream Cheese Frosting
Ingredients
- 1 ½ cups gluten free flour blend * see note
- ½ cup non-dairy milk * see note
- 1 ½ cups shredded carrot
- 1 teaspoon baking powder aluminum-free
- ½ teaspoon baking soda
- ⅛ teaspoon sea salt
- ¼ teaspoon ground allspice
- ½ teaspoon ground nutmeg
- 1 ½ teaspoon ground cinnamon
- 1 ¼ cups coconut sugar or brown sugar
- 3 large eggs
- ¼ cup coconut oil melted
- 3 ounces apple sauce unsweetened
- 3 tablespoons chia seeds
For Frosting
- 8 ounces softened cream cheese * see note
- ¼ cup unsalted butter or plant-based butter
- 1 teaspoon pure vanilla extract
- 2 cups powdered sugar
Email This Recipe To Me!
I will email this recipe to you, so you can come back to it later!
Instructions
- Move your oven rack to a middle position. Set the temperature of the oven to 350º F to preheat your oven.
- Add 1 1/2 cups gluten free flour blend, 1 teaspoon baking powder, 1/2 teaspoon baking soda, 1/4 teaspoon ground allspice, 1/2 teaspoon ground nutmeg, 1 1/2 teaspoon ground cinnamon, 3 tablespoons chia seeds, and 1/8 teaspoon sea salt to a large mixing bowl. Whisk to blend the dry ingredients together.
- In a smaller bowl, add 3 large eggs, 1 1/4 cups coconut sugar, 3 ounces apple sauce, melted 1/4 cup coconut oil, 1/2 cup non-dairy milk, and shredded 1 1/2 cups shredded carrot. Mix well with a whisk.
- 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. For best results, I do not recommend using a standing mixer because it tends to overmix your batter, making your cupcakes denser.
- Line a muffin tin with parchment paper cupcake liners and fill each 3/4 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.
- Bake your gluten free carrot cake cupcakes at 350º F for 20-25 minutes. Remove from the oven and cool before frosting.
Frosting
- Make the frosting by adding 8 ounces softened cream cheese, 2 cups powdered sugar, 1 teaspoon pure vanilla extract, and 1/4 cup unsalted butter (softened) to a stand mixer with a whisk attachment.
- Mix the frosting 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!
- 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.
Notes
- I have tested this recipe with King Arthur Measure for Measure GF, Bob’s Red Mill 1 to 1 GF blend, and Authentic Foods Multi Blend. That doesn’t mean others will not work, I just have not tested other flours.
- If your gluten free flour blend doesn’t contain Xanthan Gum or Guar Gum, please add 1 teaspoon.
- To make this recipe dairy-free, substitute the butter for vegan butter and use a dairy-free cream cheese like Kite Hill or VioLife.
- Do not use imitation vanilla.
- I highly suggest using almond flour and not an almond meal. Almond meal is more coarse and will make your donuts grainy.
- Other dairy-free kinds of milk will work but I do not recommend canned coconut milk.
- If you want your cupcakes to have a domed style top, bake at 425º F for the first 5 minutes then reduce the temperature to 350º F.
- These cupcakes will keep up to 4 days in an airtight container, or up to 4 months in the freezer.
SPECIAL NOTE
Please know that every gluten free flour blend has a different starch to grain ratio. If you use a blend I didn’t test, my rule of thumb is to add more flour if your dough or batter is wet and add more liquid if the dough or batter is too dry!
Nutrition
Nutrition Disclaimer
Nutritional information is an estimate provided to you as a courtesy. You should calculate the actual nutritional information with the products and brands you are using with your preferred nutritional calculator.
What’s wrong with raw milk?
I don’t recall talking about raw milk as an ingredient. Use what you choose to use.
I MADE THESE LAST EVENING; WITHOUT THE FROSTING; JUST SPRINKLED A LITTLE POWERED SUGAR ON THEM. THEY WERE EXCELLENT. VERY MOIST.
I am so glad you loved the recipe. These are one of my favorites as well. Thank you!
Can I make this a cake instead of cupcakes ? Have you done it ?
Hi Heidi, this recipe can easily be into a cake. The baking time will be longer, depending on the size and depth of the baking pan you use.
I love this recipe! This is a healthier option with chia seeds and still moist and delicious!
I am so glad you loved this recipe. I often need a healthier option with less sugar, so I am glad others are loving it too!
Chia seeds? When are they added?
Hi Debra, the chia seeds go in with the dry ingredients. I hope you had a nice holiday. Sandi
So almond milk or no almond milk? The ingredients list says “1/2 c almond milk” but the steps don’t say to add almond milk anywhere.
Hi Hannah, it goes in with the wet ingredients. Be sure to warm the coconut oil so it isn’t hardened by the cooler milk.
Thank you! I made these last night and they turned out great!
I am so glad you enjoyed them Hannah! Thank you for coming back to let me know!
the recipe calls for baking soda? but does not say how much?
Hi Jenni, it should be 1/2 teaspoon. Thank you!
New favorite recipe and can’t wait to make these again!! Thank you!
I am so glad you enjoyed these cupcakes. Thank you so much for coming back to let others know it is a great recipe.
What can I use instead of chia seeds? Thank you.
Hi Suzanne, you can substitute flaxseed meal in the same amount.
I haven’t made this recipe yet, but I’m confused about the mentions of almond flour. There is no almond flour in the recipe, but there are a couple notes saying that there is almond flour in the recipe. Confused!
It took me a moment to find where almond flour was mentioned. I think the sentence you saw was before I revamped the recipe. I had taken out all other references but missed that one sentence. Sorry Wren.
Hi! I had extra carrots and found out that my fiancé never had carrot cake before so I had to fix that. I’ve been gluten free for a while now but he’s just getting used to the change (since I do all the cooking). Anyway, these cupcakes were INCREDIBLE! My fiancé loved them so much and so did my roommate. I love the chia seeds and I added the flaxseed in as well from your substitution list. I can’t wait to try more of your recipes. Thank you so much for the sweet treat!
You made my day coming back to tell me how much you all liked this recipe. Thank you so much!
How do you think they would do frozen, without the icing, of course. There are only two of us, and I wouldn’t want that many cupcakes hanging around. I’m afraid they would be my breakfast, lunch and dinner!
Hi Alene, if you freeze without the frosting they will hold up very well. I freeze mine so I have a treat on-hand when I want.
I made this for my nephew’s birthday and it was really great! They did “fall” a little but they were delicious and moist without being gummy. Will definitely make them again
I am so glad everyone liked these. I really appreciate your coming and letting me know 🙂
I modified these to be muffins rather than cupcakes – 2-1/4 C flour, 2/3 C sugar + some Stevia, 2 t baking powder and skipped the apple sauce because I didn’t have any. They turned out beautifully – light pleasant texture and I love the little pops from the chia seeds! Yummy with cream cheese for breakfast.
I love that you made this recipe even better Dorothy. Thank you so much for sharing how you modified it to help other readers.
My pleasure! I forgot to say I also made them gluten free I used my own flour mix and 1-1/2 teaspoons xanthan gum