What do you do if you want a piece of one of your favorite carrot cakes in an easy grab-and-go form? Make it as cupcakes! The Best Carrot Cake Cupcakes is one of those treats for me.
These are the most moist, fluffy, and spongy soft, delicious cupcakes you'll ever try. They are made completely from scratch, down to the freshly grated carrots, and topped with a generous swirl of the absolute best cream cheese frosting!

These carrot cake cupcakes are a modified version of my favorite healthier homemade carrot cake. In this version of the recipe, I've used kefir in the recipe instead of apple sauce in the actual cake recipe and it tastes amazing.
Cupcakes are always a hit at any gathering and at my house as well. I personally love cupcakes because they are not only cute but perfectly portioned, just the right serving size and easy to eat anywhere you are. I hope you will enjoy them as well. Enjoy!
Table of Contents
📋 Recipe Ingredients
Carrot Cake Cupcake Batter Ingredient
- All-purpose flour
- Baking soda
- Baking powder
- Ground cinnamon
- Nutmeg
- Sea salt

- Eggs
- Sugar
- Kefir (or buttermilk)
- Pure Vanilla Extract
- Grated carrots

Carrot Cake Cupcakes Cream Cheese Frosting Ingredients
- Cream cheese
- Sugar
- Unsalted butter
- Greek yogurt
- Pure Vanilla Extract
- Sea salt
- Heavy whipping cream

Carrot Cake Cupcake Decoration Ingredients
- Sugar Carrot Candies
- Sparkle flakes (optional, comes with carrot candies)

🔪 Recipe Instructions
How to Make Carrot Cake Cupcake Batter
Measure out all dry ingredients: flour, baking soda, baking powder, ground cinnamon, nutmeg, and sea salt into a bowl and mix together using a hand whisker. Set aside until ready for use.

Preheat the oven to 350 F (180 C).
Beat eggs and sugar on high for 5 minutes or until fluffy and pale in color. Reduce mixing speed to medium/low and add vanilla extract and kefir. Mix for another minute or so.

Remove the bowl from the mixer stand. Using a large silicone spatula mix in half of the dry ingredients into the egg mixture, alternating with adding half of the number of grated carrots, then stirring very carefully trying not to deflate too many air pockets. Repeat the same process with the second half of the dry ingredients and carrots.

⏲️ Baking Time
Divide the batter evenly (to about half of the liner) between 24 cupcake liners. Bake for 15 minutes or until an inserted toothpick into the center of a cupcake comes out clean.
Cool cupcakes in the baking pan for about 5 - 10 minutes before transferring them onto a cooling rack. Cool completely before frosting cupcakes.

How to Make Cupcakes Cream Cheese Frosting
Beat softened cream cheese on high mixing speed for a couple of minutes, scraping down the cream cheese on the sides of the mixer bowl halfway through. Then add butter and beat again until combined.
Next, with mixing speed running on medium, add sugar, and then Greek yogurt. Beat again for about a minute, scraping down the sides of the bowl in the middle of mixing. Finally, add vanilla, salt, and beat again for another minute. The frosting will be thick and smooth.
Finally, add cold heavy whipping cream and start beating the cream slowly on low, then gradually increase the mixing speed to medium. Scrape down the cream multiple times to ensure all the ingredients are well incorporated.
NOTE: The frosting will thicken during the mixing process. Do not overbeat the frosting! As soon as it starts to hold its shape the frosting is ready.

How to Decorate Carrot Cake Cupcakes
Use a large Wilton 6A tip with a piping bag to pipe out the cream onto cooled cupcakes. Place a sugar carrot candy on top of each cupcake and sprinkle some edible sparkly glitter on top.
NOTE: The sugar carrot candies on top of the frosting will begin to melt after some time, so for the best presentation please leave this decorating step to be done no longer than 30 minutes before serving.

💭 Storing Suggestions
The frosted cupcakes can be stored in an airtight container in the refrigerator up for up 5 days. Bring them to room temperature (about an hour) before serving.
Freeze the cupcakes for up to 3 months. Thaw them overnight in the refrigerator, and bring them to room temperature before serving. Do not freeze sugar candy decor as it will melt.

Enjoy a cupcake with a cup of hot tea or a homemade latte.

👩🏻🍳 Baking Tips
- When measuring your flour for these cupcakes, make sure to spoon it into the measuring cup and level it off with the back of a knife.
- You can replace the kefir with ½ cup of apple sauce, melted butter, or olive oil.
- Use a block of cream cheese not whipped or spread in a tub.

If you make these The Best Carrot Cake Cupcakes, please share a picture with me on Facebook, Instagram, or Pinterest. Tag with #valyastasteofhome. I’d love to see your creations!
Recipe Card
The Best Carrot Cake Cupcakes
Ingredients
Carrot Cake Cupcake Batter Ingredients
- 2 ½ cups – organic all-purpose flour
- 1 tsp. – baking soda
- 1 tsp. – baking powder
- 1 tsp. – ground cinnamon
- ¼ tsp. – nutmeg
- ¼ tsp. – sea salt
- 3 large – eggs
- ¾ cup – organic sugar
- 1 tsp. – pure vanilla extract
- 1 cup - kefir
- 2 cups – grated carrots
Carrot Cake Cupcake Frosting Ingredients
- 16 oz. – cream cheese
- ½ cup – organic sugar
- 4 oz. – unsalted butter
- ½ cup – Greek yogurt plain
- ½ tsp. - pure vanilla extract
- ¼ tsp. – sea salt
- 2 cups – cold heavy whipping cream
Carrot Cake Cupcake Topping Ingredients
- Sugar carrot candies
- Sparkly edible glitter
Supplies
- 24 - cupcake liners
- 1 - (24 cupcake ) - regular muffin pan
Instructions
How to Make Carrot Cake Cupcake Batter
- Measure out all dry ingredients: flour, baking soda, baking powder, ground cinnamon, nutmeg, and sea salt into a bowl and mix together using a hand whisker. Set aside until ready for use.
- Preheat the oven to 350 F (180 C).
- Beat eggs and sugar on high for 5 minutes or until fluffy and pale in color. Reduce mixing speed to medium/low and add vanilla extract and kefir. Mix for another minute or so.
- Remove the bowl from the mixer stand. Using a large silicone spatula mix in half of the dry ingredients into the egg mixture, alternating with adding half of the amount of grated carrots, then stirring very carefully trying not to deflate too many air pockets. Repeat the same process with the second half of the dry ingredients and carrots.
Cupcake Baking Time
- Divide the batter evenly (to about half of the liner) between 24 cupcake liners. Bake for 15 minutes or until an inserted toothpick into the center of a cupcake comes out clean.
- Cool cupcakes in the baking pan for about 5 - 10 minutes before transferring them onto a cooling rack. Cool completely before frosting cupcakes.
How to Make Cupcakes Cream Cheese Frosting
- Beat softened cream cheese on high mixing speed for a couple of minutes, scraping down the cream cheese on the sides of the mixer bowl halfway through. Then add butter and beat again until combined.
- Next, with mixing speed running on medium, add sugar, and then Greek yogurt. Beat again for about a minute, scraping down the sides of the bowl in the middle of mixing. Finally, add vanilla, salt, and beat again for another minute. The frosting will be thick and smooth.
- Finally, add cold heavy whipping cream and start beating the cream slowly on low, then gradually increase the mixing speed to medium. Scrape down the cream multiple times to ensure all the ingredients are well incorporated.
How to Decorate Carrot Cake Cupcakes
- Use a large Wilton 6A tip with a piping bag to pipe out the cream onto cooled cupcakes. Place a sugar carrot candy on top of each cupcake and sprinkle some edible sparkly glitter on top.
How to Store Cupcakes
- The frosted cupcakes can be stored in an airtight container in the refrigerator up for up 5 days. Bring them to room temperature (about an hour) before serving.
- Freeze the cupcakes for up to 3 months. Thaw them overnight in the refrigerator and bring them to room temperature before serving. Do not freeze sugar candy decor as it will melt.
- Enjoy a cupcake with a cup of hot tea or a homemade latte.
Notes
- The sugar carrot candies on top of the frosting will begin to melt after some time, so for the best presentation please leave this decorating step to be done no longer than 30 minutes before serving.
- All refrigerated ingredients need to be room temperature (except heavy whipping cream) when making this recipe.
- The frosting will thicken during the mixing process. Do not overbeat the frosting! As soon as it starts to hold its shape the frosting is ready.

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