Keto Carrot Cake Cupcakes with Cream Cheese Frosting

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These keto carrot cake cupcakes are low-carb, gluten-free cupcakes made with almond flour, carrot cake protein powder, melted butter, eggs, and finely grated fresh carrots, topped with a 3-ingredient cream cheese frosting. They are sugar-free, warmly spiced with cinnamon, moist, and bake in about 15 minutes at 350°F.

Keto carrot cake cupcakes with cream cheese frosting, chopped pecans, and finely grated carrot garnish on a marble surface

These keto carrot cake cupcakes are everything a good carrot cake should be: moist and perfectly spiced with real carrots and a sweet cream cheese frosting. You might think that sugar-free means compromising, but these taste just as good as a traditional carrot cake, if not better.

This recipe is an adaptation of Keto Chow's Keto Carrot Cake created by Amanda Balle. I made them into cupcakes because sometimes baking a whole cake makes me nervous. The bundt pan, the de-panning, the hoping with everything in you that it doesn't stick. I've been baking for years and I still hold my breath every single time. Cupcakes feel more forgiving. I also melted the butter instead of just softening it. Traditional carrot cake recipes use oil, so I thought why not try melted butter in this one. They turned out super moist!

These are a great make-ahead treat for Easter, Mother's Day, or a birthday. And remember to mark your calendar for February 3rd. It's National Carrot Cake Day. If you love these, my keto carrot cake bites are another great option when you want the same flavor in a no-bake format. I hope you love these cupcakes as much as I do!

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Ingredients
Instructions
Variations
Storage
FAQ
Related
Recipe
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Ingredients

Here's what you'll need to make these:

Butter - For moisture and richness. Coconut oil or avocado oil works as a 1-to-1 substitute.
Brown and granulated sugar-free sweeteners - The combination is for sweetness and a deeper, molasses-y undertone. I used Swerve.
Eggs - For binding and lift. Room temperature works best.
Carrot cake protein powder - Adds protein, structure, and more carrot cake flavor. Use your preferred protein powder. I used Keto Chow, naturally.
Almond flour - For structure and tender texture. Weigh it for accuracy.
Baking powder - A full tablespoon, and yes, that is not a typo. For extra lifting.
Ground cinnamon - For spice. Carrot cake protein powder does the flavor lifting here. Add in ground ginger, nutmeg, and cloves for more spice.
Fresh carrots, finely grated - Add moisture and natural sweetness. Use whole carrots and grate them on the fine side of a box grater. Pre-shredded carrots are too dry.
For the cream cheese frosting, heavy cream, cream cheese, and powdered sugar-free sweetener - Just 3 ingredients!
Optional garnish, chopped pecans and finely grated carrots - For a classic finish. Optional, but they make a beautiful cupcake!

See recipe card for complete measurements below.

Instructions

These are really easy to make. And here's how to make them:

First, preheat oven to 350℉ and line muffin pan.

Almond flour, protein powder, baking powder, and warm spices measured into a glass bowl with fresh carrots nearby

Whisk dry ingredients. For even distribution!

Dry ingredients whisked together in a glass bowl with a whisk resting inside

Set aside dry ingredients. It should look like this after whisking.

Three eggs being poured over melted butter and brown sweetener in a glass mixing bowl

Whisk wet ingredients. Make sure butter is melted, but cooled first.

Dry flour mixture poured into the wet ingredients in a glass mixing bowl

Add dry to wet. Whisk or fold until completely mixed.

Smooth cupcake batter in a glass bowl with finely grated carrots being poured in from a measuring cup

Carrots! Fold in until mixed.

Carrot cake batter with finely grated carrots fully folded in, smooth and ready to scoop

Cupcake mix done! It should look like this after mixing.

Twelve cupcake liners filled with carrot cake batter in a muffin tin, ready for the oven

Scoop into cupcake liners. Fill ⅔ full.

Twelve golden brown carrot cake cupcakes fresh from the oven in a USA Pan muffin tin

Bake 15 minutes at 350℉. Until golden brown.

A single unfrosted carrot cake cupcake on a marble board with bowls of finely grated carrots and chopped pecans nearby

Cool completely. Wire racks are great for this.

A single carrot cake cupcake with a swirl of cream cheese frosting, finely grated carrots, and chopped pecans on top

Make frosting. Pipe, top, enjoy!

Tip #1: Room temperature ingredients always work best in gluten-free baking.

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Tip #2: A cookie scoop makes filling the liners much faster and helps the cupcakes bake more evenly. I use a large scoop (about 3 tablespoons) and it's the right amount for filling each liner about ⅔ full.

Tip #3: Cool completely before frosting. I know it's hard to wait! This cream cheese frosting will slide right off a warm cupcake. Put the frosting in the fridge while you wait and they'll set up perfectly.

A hand holding a carrot cake cupcake with a bite taken out, showing the moist, tender crumb

The perfect bite!

Variations

Here are a few easy ways to change up this recipe:

Add more spice. The protein powder carries a lot of the carrot cake flavor, but if you want a more pronounced spice profile, add ¼ teaspoon each of ground ginger, nutmeg, and cloves to the dry ingredients.
Add mix-ins. Fold ¼ cup of chopped pecans or walnuts directly into the batter before baking for extra crunch in every bite.
Substitute the butter. Coconut oil works well here in a 1-to-1 swap. The butter gives a richer flavor, but coconut oil (or another neutral oil) still makes a moist cupcake.
Skip the frosting. Without the cream cheese frosting, these work as a satisfying carrot cake muffin for breakfast or a grab-and-go snack.

Try my keto chocolate flaxseed muffins too!

Storage

Store these cupcakes in an airtight container in the refrigerator for up to 3 days. Because of the cream cheese in the frosting, they need to stay cold. Pull them out about 10 to 15 minutes before serving so they're not ice cold straight from the fridge.

To freeze unfrosted cupcakes: Let them cool completely, then seal in an airtight container or freezer bag and freeze for up to 3 months. Let them thaw at room temperature for about an hour, then frost before serving.

Overhead view of a frosted carrot cake cupcake with cream cheese frosting and chopped pecans on marble

Six frosted carrot cake cupcakes on a marble board with small bowls of carrots and pecans and pink flowers in the background

FAQ

Are carrots okay on keto?

Yes, in moderation. Carrots have more carbs than some other vegetables, but a small amount spread across an entire batch of cupcakes is very manageable. This recipe uses ½ cup of finely grated fresh carrots for 12 cupcakes.

Can I use a different protein powder?

You can use about ½ cup of your preferred protein powder, but the flavor and texture may change since Keto Chow is a keto meal mix rather than a plain protein powder. It contains xanthan gum and acacia gum for binding and a built-in carrot cake spice flavor. If you substitute a plain powder, add more warm spices like cinnamon, ginger, nutmeg, and cloves to compensate, and note that your nutrition facts will change significantly.

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