These gluten-free carrot cake cupcakes are incredibly moist, packed with warm spices, and topped with tangy cream cheese frosting. They bake in just 20 minutes, which makes them perfect when you need a quick dessert for a party or celebration.
I love making cupcakes instead of layer cakes when I’m entertaining. There’s no stacking, no crumb coating, and everyone gets their own perfect portion. Plus, they’re easy to grab and eat without needing a plate.
The secret to keeping these cupcakes so moist is using oil instead of butter and adding applesauce. Oil creates a lighter, more tender crumb and keeps the cupcakes soft for days. You can even serve them straight from the fridge and they’re still perfectly tender.
Why You’ll Love this Recipe
Searching for more gluten-free cake recipes? Gluten-Free Vanilla Cake / Gluten-Free Chocolate Cake / Gluten-Free Red Velvet Cake / Gluten-Free Banana Cake
Ingredients
Ingredient Notes
- Fresh shredded carrots – Always shred your own carrots instead of buying pre-shredded. Pre-shredded carrots are dry and won’t give you the same moist texture. You need about 2 to 3 large carrots to get 2 cups shredded. You can use a box grater or a food processor with the grater attachment.
- Gluten-free flour blend – I’ve tested this with Bob’s Red Mill 1-to-1 Gluten-Free Flour (in the blue bag) and King Arthur Measure-for-Measure Gluten-Free Flour. Both blends already contain xanthan gum, so you don’t need to add extra. I haven’t tested other brands, so I can’t guarantee the results will be the same.
- Oil – Oil makes these cupcakes light and tender, and they stay soft even when stored in the fridge. Use a neutral oil like vegetable oil or avocado oil.
- Apple cider vinegar – A small amount of vinegar reacts with the baking soda to help the cupcakes rise properly. You won’t taste it at all.
Recipe FAQs
Cream cheese frosting is the classic choice and my favorite. The tangy cream cheese balances out the sweet cake perfectly. You can also use brown butter cream cheese frosting, cinnamon buttercream, or maple buttercream.
Yes! I have a gluten-free carrot cake recipe that’s specifically designed for layer cakes. The ratios are slightly different from this cupcake recipe.
Absolutely. You can stir up to 2 cups total of mix-ins into the batter. Try chopped walnuts or pecans (1 cup), raisins (3/4 cup), drained crushed pineapple (8 oz can), or shredded coconut (1/2 cup).
I’ve only tested this recipe with Bob’s Red Mill 1-to-1 Gluten-Free Baking Flour (in the blue bag, not red) and King Arthur Measure for Measure Gluten-Free Flour, so I can’t guarantee other blends will work the same way. If you try a different blend, make sure it contains xanthan gum.
Expert Tips
Storage instructions
In the Refrigerator
Store cupcakes in an airtight container in the refrigerator for up to 4 days. Let them sit at room temperature for 15-20 minutes before serving for the best texture.
In the Freezer
Freeze cupcakes for up to 3 months. Place them on a baking sheet and freeze for 1 hour until solid, then wrap individually and place in a freezer-safe container or bag. Thaw in the refrigerator overnight, then bring to room temperature before serving.
More gluten-free cakes to try
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Gluten Free Carrot Cake Cupcakes
Ingredients
For the Carrot Cupcakes:
- 1 1/2 cups (300 g) granulated sugar
- 3 (150 g) large eggs - at room temperature
- 1/2 cup (109 g) vegetable oil - or other neutral tasting oil
- 1/2 cup (125 g) unsweetened applesauce
- 2 teaspoons pure vanilla extract
- 1 teaspoon apple cider vinegar
- 1 1/2 cups (210 g) gluten free flour blend - I used Bob's Red Mill 1-to-1 Gluten-Free Baking Flour (in the blue bag) which already contains xanthan gum
- 1/2 Tablespoon baking powder
- 1 teaspoon baking soda
- 2 teaspoons ground cinnamon
- 2 teaspoons ground ginger
- 1 teaspoon ground nutmeg
- 1/4 teaspoon ground cloves
- 1/2 teaspoon kosher salt
- 2 cups (250 g) finely shredded carrots - about 2-3 large carrots
For the Cream Cheese Frosting:
- 4 oz (113 g) butter - softened to room temperature
- 8 oz (226.8 g) cream cheese - softened to room temperature
- 1 teaspoon pure vanilla extract
- 3 cups (360 g) powdered sugar - up to 4 cups as needed
**Use the toggle button above to turn the instruction photos on and off!
Instructions
For the Cupcakes:
- Preheat oven to 350°F. Line two 12-cup muffin tins with cupcake liners. Set aside.
- In a large bowl, beat together 1 1/2 cups (300 g) granulated sugar and 3 (150 g) large eggs for 2 minutes with an electric mixer, until the mixture is light in color and well combined.
- Add the 1/2 cup (109 g) vegetable oil, 1/2 cup (125 g) unsweetened applesauce, 2 teaspoons pure vanilla extract, and 1 teaspoon apple cider vinegar. Mix until smooth and combined.
- In a medium bowl, whisk together 1 1/2 cups (210 g) gluten free flour blend, 1/2 Tablespoon baking powder, 1 teaspoon baking soda, 2 teaspoons ground cinnamon, 2 teaspoons ground ginger, 1 teaspoon ground nutmeg, 1/4 teaspoon ground cloves, and 1/2 teaspoon kosher salt.
- Gradually add the dry ingredients to the wet ingredients, mixing between each addition, until no streaks of flour remain. Don’t overmix.
- Stir in 2 cups (250 g) finely shredded carrots until evenly distributed throughout the batter.
- Fill each cupcake liner about 3/4 full. I use a cookie scoop to make this easier and keep them all the same size.
- Bake at 350°F for 18-22 minutes, until a toothpick inserted into the center of a cupcake comes out clean. Remove from the oven and let cool completely on a wire rack before frosting.
For the Cream Cheese Frosting:
- While the cupcakes are cooling, make the frosting. In a large bowl, beat 4 oz (113 g) butter and 8 oz (226.8 g) cream cheese together with an electric mixer until completely smooth, about 2-3 minutes.
- Mix in 1 teaspoon pure vanilla extract.
- Gradually add 3 cups (360 g) powdered sugar, a little at a time, mixing on low speed after each addition. Add 3 to 4 cups total, until you reach your desired consistency. The frosting should be thick and smooth.
- Frost the cooled cupcakes using a knife or pipe rosettes on top using a pastry bag with a 1M tip.
- Serve immediately or store in the refrigerator. Keep leftovers in an airtight container in the refrigerator for up to 4 days or in the freezer for up to 3 months.
Notes
- Flour: This recipe was tested with Bob’s Red Mill 1-to-1 Gluten-Free Baking Flour, which already contains xanthan gum. I haven’t tested other blends, so results may vary with different brands.
- Measuring flour: For best results, use the metric measurements provided. If measuring by cups, spoon the flour into your measuring cup and level it off with a straight edge. Don’t scoop directly with the cup, as this packs in too much flour.
- Shredding carrots: Use fresh carrots that you shred yourself. Pre-shredded carrots from the store are too dry and won’t give you moist cupcakes.
- Storage: Store frosted cupcakes in an airtight container in the refrigerator for up to 4 days. Let sit at room temperature for 15-20 minutes before serving.
- Freezing: Flash freeze cupcakes on a baking sheet for 1 hour, then wrap individually and store in a freezer-safe container for up to 3 months. Thaw in the refrigerator overnight.
These are practically healthy! Looks amazing and I can’t wait for my birthday 🙂
So yummy!
So glad you enjoyed these Nicole! They’re one of my favorites!
I’m hoping to make this recipe as one of several for my wedding reception! I’m wondering if you think it would be okay to freeze the batter for a few days, thaw, and then bake? Obviously I’ll test it first, but thought I’d ask for any tips & tricks you might have!
Hi Annaka, I haven’t tried freezing the batter, but I think the cupcakes will be too flat if you do this because the leavener will have already reacted with the acid. Instead, I would recommend baking the cupcakes ahead of time and then flash freezing them for an hour and then cover them in a freezer-safe container or bag and freeze up to 2 months. You can just let them thaw for about 30 minutes before frosting. You can also freeze them with the frosting, they’re just a bit more finicky if you plan on stacking them in the freezer the frosting can get messed up sometimes. Hope this helps! Let me know if you have other questions and Congratulations to you!
These are the most delicious GF I’ve ever made and even all my non GF people love them too! I was wondering if I could swap pumpkin purée instead of carrots for a pumpkin spice cupcake. Would it be a straight swap of 2 cups do you think??
Hi Holly! I’m glad you love the carrot cake cupcakes! I think swapping the carrot for pumpkin might result in too much moisture. You’d probably need to omit the applesauce and the carrots to get the moisture content closer. I have pumpkin cupcakes on my list to develop, so I’ll try to get to those sooner and report back! Otherwise, I know Iowa Girl Eats has a fabulous gluten-free pumpkin cupcake recipe you may want to try in the meantime!
These cupcakes were amazing. I made them for my father in law whose GF and it’s his favorite dessert. He said they were the best cupcakes he’s ever had. They were so tender and moist and full of flavor!
So glad your father in law enjoyed these, Bek! They’re my favorite cake recipe!
Thank you for sharing this recipe! After wasting ingredients on another failed gluten free carrot cake, cupcake recipe, I was feeling very defeated. I had to call it a day last night after being in the kitchen for 10 hours. I had to have this ready for pick up for an order on Thursday. So I got up early this morning made a half of the recipe, to see how it would turn out, and it turned out fabulous! Thank you so much for sharing your recipe! I hope my customers are just as happy as I was! I did change the sugar content and used 1/2 cup of brown sugar instead of all white sugar. I also didn’t have apple cider vinegar on hand, so I used white balsamic vinegar with a dash of Graventine apple balsamic reduction that I had on hand.
Thanks again! Schel! 🥰
I’m so glad you gave my recipe a try, Schel! I love your additions as well! Thanks for coming back to let me know – I hope your customers enjoy them!
Hey I was wondering what to do if I don’t have Apple sauce? -so far so good btw! 😋
I haven’t tried it in this recipe, but Greek yogurt or sour cream should work well as a substitute! The applesauce helps with moisture and adds a bit of sweetness, so just keep in mind the cupcakes might be slightly less sweet with those swaps. Let me know how it goes if you try it!