Keto Carrot Cake Cupcakes Recipe With Cream Cheese Frosting

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This keto carrot cake recipe is irresistible and guilt-free. Moist and flavorful cupcakes topped with creamy cream cheese frosting are the perfect way to satisfy your sweet tooth while staying low-carb.

Keto carrot cake recipe with cream cheese frosting.
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At the end of last year, I asked followers and subscribers what they wanted to see more of from me in the coming year. 

Among the responses, one request stood out loud and clear…more healthy, yet still delicious recipes. Let me tell you, your wish is my command!

I’m all about enjoying the coziness of homemade comfort food, however I also understand the importance of nourishing our bodies with wholesome, delicious, nutrient rich foods as well. 

After all, why does healthy eating have to mean sacrificing flavor or satisfaction?

Keto carrot cake cupcakes are the epitome of comfort in every bite, combining the cozy flavors of carrot cake with the guilt-free goodness of a keto friendly dessert.

They’re moist, spiced to perfection, and topped with a generous swirl of creamy cream cheese frosting; all while being low in carbs and sugar.

Whether you’re following a ketogenic diet or simply looking for a healthier alternative to a classic carrot cake, these cupcakes are going to satisfy your cravings and your sweet tooth. 

So let’s gather the ingredients, preheat the oven, and get ready to enjoy a taste of comfort, keto-style!

Low carb carrot cake recipe with luscious cream cheese frosting.

What you’ll love about this recipe:


  • IRRESISTIBLE FLAVOR – Each bite offers a combination of warm, comforting flavors that will leave you craving more.
  • TENDER TEXTURE – The almond flour and grated carrots work together to create a delightful texture that’s both satisfying and indulgent.
  • HEALTHY INGREDIENTS – These cupcakes are low in carbs and sugar, making them perfect for those following a keto lifestyle or anyone looking to enjoy a healthier dessert option.
  • CREAM CHEESE FROSTING – Let’s be honest…what’s carrot cake without the cream cheese frosting?! This recipe takes it up a notch with a delicious & tangy cream cheese frosting that perfectly complements the sweetness of the cupcakes.

Ingredients You’ll Need to Make Low Carb Carrot Cake Cupcakes

A traditional carrot cake recipe is a classic favorite for many, but it often contains tons of sugar and carbs.

Easy keto carrot cake cupcakes made with shredded carrots and almond flour.

With a few clever substitutions and tweaks, you can enjoy all the goodness of carrot cake without compromising your low carb diet. 

This Keto carrot cake recipe is the perfect solution!

Jump to Recipe

Carrot Cake Cupcakes

  • Salted Butter: I like to use salted butter but you can use also use unsalted butter, just add 1 teaspoon kosher salt to the recipe.
  • Granulated Sweetener (Sugar Substitutes: Monk fruit, Erythritol, or Xylitol): This sugar alternative adds just the right amount of sweetness.
  • Large Eggs: Make sure the eggs are at room temperature to ensure a lighter cake. 
  • Plain Greek Yogurt: Enhances the texture of the cupcakes and provides a subtle tanginess that complements the sweetness of the carrots and spices.
  • Pure Vanilla Extract: Adds a warm, aromatic flavor. I like to make my own vanilla extract for even more depth of flavor.
  • Superfine Almond Flour: I recommend a finely ground almond flour for the best cake texture.
  • Baking Soda & Powder: The combination of these two ingredients will help the cupcakes rise.
  • Pumpkin Pie Spice: This spice will add warmth to the cupcakes. If you do not have pumpkin pie spice on hand, you can use 1 ½ teaspoons of cinnamon, ¼ teaspoon nutmeg, and ¼ teaspoon ginger instead.
  • Shredded Carrots: You’ll want to shred your own carrots for this recipe. The pre-shredded carrots you can purchase at the grocery store are too dry and won’t incorporate well into the cake batter.
  • Finely Chopped Pecans: These will add texture to the cupcakes, but can be omitted or substituted with chopped walnuts if you prefer.

Be sure to check out the full recipe and ingredient list at the end of this blog post.

Keto Cream Cheese Frosting

  • Cream Cheese: Gives the frosting that tangy flavor.
  • Salted Butter: Feel free to use unsalted butter, just add a pinch of salt to balance the sweet flavors.
  • Powdered Monk Fruit Sweetener: This powdered sweetener is perfect for this fluffy cream cheese frosting.
  • Heavy Whipping Cream: Adds richness & creaminess to the frosting.
  • Pure Vanilla Extract

Carrot Topper

  • Green & Orange Gel Food Coloring: This is completely optional, but adds charming little carrots to the top of your finished cupcakes.

TOOLS YOU’LL NEED

How to Make This Easy Keto Carrot Cake Recipe

With your ingredients in hand, here’s how to whip up a batch of these mouthwatering low-carb carrot cake cupcakes.

Step 1: Preheat the Oven

Preheat oven to 350 degrees. Line a cupcake pan with liners or spray with nonstick cooking spray.

Step 2: Mix the Carrot Cake Batter

In a medium mixing bowl whisk the flour, baking soda, baking powder, and pumpkin pie spice until fully combined. Set aside.

Mixing bowl with dry ingredients like almond flour, baking soda & powder, and pumpkin pie spice.

In a large mixing bowl, using a hand mixer or a stand mixer, combine butter and monk sugar until fully combined. Scrape down the sides of the bowl, as necessary. 

Mixing wet ingredients with a hand mixer to incorporate the eggs and butter.

With mixer on low add eggs, one at a time. Next, add in Greek yogurt and vanilla extract. Mix until combined.  

Hand mixer mixing eggs into carrot cake batter for keto cupcakes.
Mix Greek Yogurt into keto carrot cake batter to create fluffy cupcakes.

Add the flour mixture to the wet ingredients, blend well. 

Gently stir carrots and pecans into flour and egg mixture just until combined, making sure not to overmix the batter.

Shredded carrots and chopped pecans in the cake batter.
Shredded carrots mixed into carrot cake batter to make keto cupcakes.

Step 3: Bake the Cupcakes

Scoop cake batter into a prepared muffin pan, filling each one about ¾ full.

Bake 18-22 minutes or until a toothpick inserted into cupcake comes out clean. 

Low carb carrot cake cupcakes in muffin pan cooling on a wire rack.

While the cupcakes bake, make the cream cheese frosting.

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Step 4: Make the Rich Cream Cheese Frosting

In a large bowl with a mixer, mix together cream cheese and butter for about 1-2 minutes.

Beat butter to start the rich cream cheese frosting recipe.

Slowly add in the powdered sugar substitute and mix an additional 2-3 minutes.

Powdered sweetener in keto cupcakes for sweetness.

Add in heavy cream and vanilla extract, mixing on high for an additional 3-4 minutes or until mixture becomes light and fluffy.

Mixing vanilla extract into cream cheese frosting for depth of flavor.
The completed cream cheese frosting for carrot cake cupcakes.

Step 5: Frost & Decorate the Carrot Cake Cupcakes

Allow cupcakes to cool completely before frosting.

Pipe or spread a layer of frosting onto cooled cupcakes and decorate as desired.

I thought adding a little frosting carrot on top was a charming addition to these delicious cupcakes.

Enjoy!

Delicious keto carrot cake recipe will become your favorite cake anytime of the year.

Tips & Tricks

  • Grate the carrots finely for the best texture and flavor. This allows them to easily blend into the batter and ensures even distribution throughout the cupcakes. Do not use store bought shredded carrots!
  • When combining the wet and dry ingredients, mix until just combined. Overmixing can lead to dense and tough cupcakes.
  • Make sure your butter and eggs are at room temperature. Room temperature ingredients will yield you a light and airy cake texture.
  • Fill each cupcake liner about 2/3 full with batter. Using an ice cream scoop or a measuring cup will help ensure each cupcake is the same size.
  • Let the cupcakes cool completely on a wire rack before frosting them. Frosting warm cupcakes can cause the frosting to melt and slide off.
A dozen delicious keto carrot cake cupcakes with rich creamy frosting.

Carrot Cake Cupcake Substitutions & Variations

Here are some recipe variations and substitutions you can try to customize these keto carrot cake cupcakes…

Nut Free: If you’re allergic to nuts or prefer to avoid them, you can use sunflower seed flour in place of the almond meal. You can also omit the chopped pecans from the recipe.

Note: Coconut flour will not work in this recipe.

Dairy Free: While Greek yogurt adds moisture and richness to the cupcakes, you can substitute it with a dairy-free alternative like coconut or almond milk. 

Cake Batter Mix-ins: Customize your cupcakes with additional mix-ins like shredded coconut, chocolate chips, raisins, or even a hint of orange zest for extra flavor.

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Spices: This recipe calls for pumpkin pie spice, but you can also use a combination of cinnamon, nutmeg, and ginger. If you have apple pie spice in your cabinet you can even use that too!

Sour Cream Instead of Cream Cheese: If you don’t have cream cheese on hand or want a twist on the classic cream cheese frosting, use sour cream instead.

Mini Cupcakes: Turn these cupcakes into miniature form by using a mini muffin tin, just make sure to adjust the baking time accordingly.

Mini keto carrot cake cupcakes are perfect for snacking or serving in a dessert sampler.

Almond flour carrot cake cupcakes with rich cream cheese frosting.

FAQs: Keto Carrot Cake Recipe

Yes, you can use your sweetener of choice instead of a keto friendly sweetener like monk fruit. However, keep in mind that regular sugar will significantly increase the carbohydrate content of the cupcakes and won’t be suitable for a keto diet.

Absolutely! While the cream cheese frosting adds a delicious finishing touch to the cupcakes, you can omit it all together or if you’re looking to reduce the overall calorie and fat content of the recipe. Without the frosting you’ll essentially have carrot cake muffins…yum!

You can bake the cupcakes ahead of time and store them in an airtight container in the refrigerator for up to several days. For best results, don’t frost them until just before serving to maintain the freshness of the luscious cream cheese frosting.

What is the best way to store leftover carrot cake cupcakes?

You can store your leftover cupcakes in the refrigerator for up to 4 days covered with plastic wrap or in an airtight container. 

If you want them to last longer, they can be frozen in an airtight container for up to 3 months and defrosted the day before you plan to eat them.

Use root vegetables like carrots to make delicious, comforting cupcakes.

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xoxo, heidi

Low carb carrot cake recipe with luscious cream cheese frosting.
5 from 3 votes

Keto Carrot Cake Cupcakes With Cream Cheese Frosting

Find the ultimate guilt-free dessert with these keto carrot cake cupcakes. Moist, spiced, and topped with a creamy cream cheese frosting, each bite is bursting with flavor without compromising on carbs.
Print Recipe
Prep Time:32 minutes
Cook Time:20 minutes
Total Time:52 minutes

Ingredients

For the Cupcakes

  • ½ cup Salted Butter softened
  • ¾ cup Granulated Sweetener Monk fruit, Erythritol, or Xylitol
  • 3 Large Eggs room temperature
  • ½ cup Plain Greek Yogurt
  • 1 tsp Pure Vanilla Extract
  • 2 ½ cups Superfine Almond Flour spooned & leveled
  • 1 tsp Baking Soda
  • 1 tsp Baking Powder
  • 2 tsp Pumpkin Pie Spice
  • 1 ½ cups Carrots peeled & shredded
  • ½ cup Pecans finely chopped

For the Cream Cheese Frosting

  • 8 ounces Cream Cheese softened
  • 1/2 cup Salted Butter softened
  • 1 1/2 cups Powdered Monk Fruit Sweetener
  • 1/4 cup Heavy Whipping Cream
  • 1 tsp Pure Vanilla Extract

For the Carrot Topper

  • Green & Orange Gel Food Coloring

Instructions

  • Preheat oven to 350 degrees. Line cupcake pan with liners or spray with nonstick cooking spray.
  • In a medium mixing bowl whisk the flour, baking soda, baking powder, and pumpkin pie spice until fully combined. Set aside.
  • In a large mixing bowl, using a handheld mixer or a stand mixer, combine butter and monk sugar until fully combined. Scrape down the sides of the bowl, as necessary.
  • With mixer on low add eggs, one at a time. Next, add in Greek yogurt and vanilla extract. Mix until combined.
  • Add the flour mixture to butter & egg mixture, blend well.
  • Gently stir carrots and pecans into flour and egg mixture just until combined, making sure not to overmix the batter.
  • Scoop cake batter into a prepared muffin pan, filling each one about ¾ full.
  • Bake 18-22 minutes or until a toothpick inserted into cupcake comes out clean.
  • While the cupcakes bake, make the cream cheese frosting.
  • In a large bowl with a mixer, mix together cream cheese and butter for about 1-2 minutes.
  • Slowly add in the powdered sugar substitute and mix an additional 2-3 minutes.
  • Add in heavy cream and vanilla extract, mixing on high for an additional 3-4 minutes or until mixture becomes light and fluffy.
  • Allow cupcakes to cool completely before frosting.
  • Pipe or spread frosting onto cooled cupcakes and decorate as desired. I thought adding a little frosting carrot on top was a charming addition to these delicious cupcakes.
  • Enjoy!

Notes

  • Grate the carrots finely for the best texture and flavor. This allows them to easily blend into the batter and ensures even distribution throughout the cupcakes. Do not use store bought shredded carrots!
  • When combining the wet and dry ingredients, mix until just combined. Overmixing can lead to dense and tough cupcakes.
  • Make sure your butter and eggs are at room temperature. Room temperature ingredients will yield you a light and airy cake texture.
  • Fill each cupcake liner about 2/3 full with batter. Using an ice cream scoop or a measuring cup will help to make uniformly sized cupcakes.
  • Let the cupcakes cool completely on a wire rack before frosting them. Frosting warm cupcakes can cause the frosting to melt and slide off.

Nutrition

Serving: 1cupcake | Calories: 313kcal | Carbohydrates: 7g | Protein: 10g | Fat: 28g | Fiber: 3g
Course: Dessert
Cuisine: American
Keyword: Carrot Cake, Cupcakes, Keto
Servings: 12 cupcakes
Calories: 313kcal

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Keto carrot cake recipe with cream cheese frosting.
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3 Comments

  1. 5 stars
    This recipe is delicious! The carrot cake cupcakes are moist and the frosting is the perfect finishing touch. I’ll definitely make this recipe again.

5 from 3 votes (1 rating without comment)

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