Keto and Sugar Free Carrot Cake Cupcakes with Cream Cheese Frosting
This Keto and Sugar free Carrot Cake Cupcake recipe takes an American classic and makes it low carb and gluten free friendly. One of my all time favorites. A moist and perfectly spiced almond flour cupcake topped with a rich and creamy cream cheese icing.

If you grew up in America, you are familiar with carrot cake. It is especially popular this time of year when Springtime is approaching. Let us forget about our troubles for 1 hour and make keto carrot cake muffins!
Perfectly spiced cupcakes with carrots
Yes, carrots. 1 whole cup to be exact so it will not impact the carb count too much. I used pre-shredded carrots from the grocery store but you can definitely shred your own.
The pre-shredded carrots were a little thick so I pulsed them in a mini food processor. You can see the texture I was left with in the photo below.

What’s that sour cream in the bowl? Actually, it is Greek Yogurt.
I love the fluffiness I get in my muffins by adding Greek Yogurt and then using baking soda to lift them right up into fluffy pillows.
This almond flour cupcake recipe is one I have been using for all of my keto muffins and cupcakes. I love the results so it is easy to add different flavors for different results. Like adding chocolate chips for my keto chocolate chip muffins, adding banana extract and walnuts for my keto banana bread muffins, adding blueberries to make keto blueberry muffins, and adding some spices and carrots for this sugar free carrot cake cupcake recipe.
Alternative for almond flour
Coconut flour is the common alternative but it is not my favorite. It is like a sponge and the liquid ingredients would need to be increased to compensate so I do not recommend it.
I have heard good things about sunflower seed flour being a good 1 for 1 substitute for almond flour. If you have an almond allergy, be sure to try it out.
This recipe makes 12 cupcakes and the batter is the perfect amount to fill each cupcake liner.
A quick tip for cupcakes that peel right out of the liners – spray the insides with cooking spray!

Cream cheese frosting
Do you call it frosting or icing? I’m from the South so for me, it’s icing!
Sugar free carrot cake muffins require cream cheese icing, in my opinion.
If you have a favorite cream cheese frosting recipe that uses only cream cheese, butter, vanilla, and sugar…simply replace the sugar with sugar free powdered sweetener and you are all set.
That’s all I did for this cream cheese frosting recipe and the results were perfect.
I am no cupcake piping expert so my keto carrot cake cupcakes look nice and rustic.
I made them prettier by topping them with a crumble made out of shredded carrot, chopped walnuts, and shredded carrots.


Keto Carrot Cake Cupcakes with Cream Cheese Frosting
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Ingredients
Muffins:
- 2 1/2 Cups almond flour (see my favorite on Amazon)
- 1 teaspoon Baking soda
- 1/4 teaspoon Kosher salt
- 1/2 Cup sugar free granulated sweetener (see my favorite on Amazon)
- 3 Large eggs, beaten
- 1 Cup Shredded carrots
- 1 1/2 teaspoon Cinnamon
- 1/2 teaspoon Ground ginger
- 1/4 teaspoon Nutmeg
- 8 oz Greek Yogurt
- pinch of salt
- 2 teaspoons Vanilla Extract
Frosting:
- 8 ounces Cream cheese, softened
- 1/2 Cup Butter, softened
- 1 teaspoon Vanilla
- 1 cup sugar free powdered sweetener
Garnish: (optional)
- 1 Tablespoon sugar free granulated sweetener (see my favorite on Amazon)
- 1 Tablespoon Walnuts
- 1 Tablespoon Shredded carrots
Instructions
Muffins:
- Preheat the oven to 400F and line a 12 cup muffin pan with liners. Spray the inside of the liners with cooking spray.
- In a large mixing bowl, combine the almond flour, baking soda, salt, sweetener, vanilla cinnamon, ground ginger and nutmeg. Now add in the beaten eggs, greek yogurt and carrots. Mix well.
- Scoop the batter into the muffin cups evenly using a scoop. Bake in the oven for 18 minutes or until a toothpick comes out clean. Cool completely before frosting
Frosting:
- In a medium size mixing bowl, whip the softened cream cheese and butter. Add in the sweetener 1/3 at a time until fully incorporated. Finally, add in the vanilla and beat until nice and smooth. Use a piping bag or the corner of a a zip top bag to frost your cupcakes.
Garnish:
- Combine sweetener, walnuts, and shredded carrots in a mini food processor and pulse for a few seconds. Just enough to combine all the ingredients together and to chop up carrots and walnuts. Alternatively, you can chop finely with a knife. Garnish on top of your muffins.
Notes
- Carrots: I used pre-shredded and then chopped them even more in a mini food processor.
- Greek Yogurt: look for a plain Greek Yogurt that has the fewest carbs. This is usually 7g per cup. You can substitute sour cream but that will increase the calorie count.

My family and I absolutely loved this recipe!
We used half the sweetener in the frosting, because we do not like things too sweet.
It was so delicious!!!
Thank you!!!
These are the Best Carrot Cake muffins ever! You would never know they are Keto! I use sugar free Vanilla Greek yogurt, so, so good!
This is my first rave on a food blog…but this is an outstanding recipe! I made it as a cake for a few Keto friends last night
(where did my muffin pan go?)
And it was absolutely as good as any carrot cake we’ve had-Keto or non. I added 1/2 cup pecans and 1/2 teaspoon cardamom to the batter and baked it in an 8.5” round pan with parchment on the bottom at 350° for 40 minutes.
I used only half the sweetener in the icing.
Great texture, outstanding flavor…a hit!
I added walnuts and a few golden raisins. I was able to make 18! They are so most and delicious! Thank you!
Can we substitute sweetener with honey??
No sorry, that will not work. It needs to be a granulated sweetener.
Delicious!!! Can they stay out for 2 to 3 days or do they need to be refrigerated?
Hi do these freeze well?
My father in law is in the hospital so we can only bring one every so often.
I wanted to bake a few batches for my mother in law to store in her freezer and then bring one as needed
Thanks ????
Yes! I have frozen them very successfully!
Hello, is the nutrition facts for a single serve Cupcake?
yes
Hi Jennifer,
I have made MANY different types of keto GF muffins but this recipe is by far the best (even without the frosting for breakfast).
What I love:
-keto and gluten free
-recipe makes a full dozen – no need to skimp on batter when filling the muffin cups (my pet peeve)
-no butter or oil to mess with
-texture and taste
What I wish:
-a vegan version so my vegan friends could experience this muffin! I’ve tried flax eggs or egg replacer in other muffin recipes and can’t get past the gumminess.
I do need to work on that. My husband has a very strong egg, gluten, and milk allergy!
What kind of Greek yogurt do you use?
I use fate free plain Greek Yogurt. Either Oikos or Fage
Delicious!!! Unrelated question: do know of a good substitution for coconut flour? Thank you
These were amazing. Can you please let me know how to store them and how long they last?
I would store them in the fridge for up to 1 week.
What about adding unsweetened applesauce?
I am not sure as I haven’t tried it. Let me know how it works!
These are the best keto dessert EVER!!! I can’t wait to make different varieties….
Merciiii ????????♥️
Love the carrot cake cupcakes and icing! Big hit! Do you think I could bake this in 9 inch cake pans instead? How many layers would I get? How long to bake them and at what oven temp? Thank you, Jennifer!!
These were amazing!!!
This is our go-to dessert for our family gatherings. Several folks are keto and a couple are gluten intolerant…Delicious and so satisfying. I’ve made them many times and they are always perfect. Thanks so much for the recipe
Wasn’t sure i could stick to keto but these have changed my mind. As good as any regular carrot cake and probably lighter. I added lemon essence to the frosting instead of vanilla. Gorgeous.
I am excited to try this ! I am adjusting the recipe for 7000ft. Altitude . Do you have any suggestions? I have adjusted the flour, sugar and baking soda. I wask wondering if I should add more Greek yogurt? Thank you !
I am not sure, sorry I can’t be of more help!
Hubby approved! They were great! Easy to make- so moist! Just the exact right amount of carrot cake spice. I didn’t have Lakanto confectioners sweetener on hand to make icing, so I substituted Swerve confectioners sweetener! Wonderful! Put walnut half and tiny amt Lakanto granular on top of icing.Oh my! It was sooo good!!
I made this for Easter. Everyone love it even the non low carb eaters. I did it in a loaf pan and baked for 45 minutes. I will definitely make again!
Came out Amazing!
Thank You ????
There are delish and will be making them again ????
Best keto carrot cupcakes ever from the texture of the dough to the final product, the taste everything is pure perfection. I will no longer search for another keto carrot cake recipe. The greek yogurt made a big difference.
Thank you for sharing. I do appreciate you!
for non keto and non gluten intolerant people, can normal flour be used at the same amount?
thanks!
I have made these three times and they are sooo yummy! The third time I shredded the carrots extra fine and added a little flax meal as well as some raisins. I find they come out the best with extra fine almond flour over almond meal . Great recipe
Muffins sank!! Probably should have had baking soda in recipe.
These do use baking soda
That was delicious! So fluffy and light, but moist too! Yummy. Thank you!
This recipe is phenomenal!!!!
I made these for my husband’s birthday, he took a bite and asked, “are these real?”. Lol. Like, this is really keto???
Absolutely fantastic and will save recipe and use again and again and again.
Thank you!!!
These are amazing!
How would you recommend to store them?
Did you use regular salted butter or unsalted?.
I use salted but I think it is a personal preference!
Hi
Can the carrot cupcakes be frozen?
Definitely! I would flash freeze them on a plate for 2 hours
Hi Jennifer
I’ve made your broccoli cheese soup and chocolate cupcakes with the buttercream frosting and my husband and I loved them. I will be making other of your recipes, not disappointed yet! I follow keto eating style for a year now and love it. I will soon make your carrot cake muffins. Thank you
question
For the frosting recipe I only have swerve confectioners on hand . How much should I use -1 cup or does it need to be less?
Thanks
Yes, 1 cup
Can you bake this as a cake instead of cupcakes?
I think that would work! Use a loaf pan and bake for 30-45 minutes until a toothpick comes out clean
I am making these today, they look amazing!
Delicious, healthy and amazing ingredients. Best time to try your recipe for Easter tomorrow.
Hi Jennifer, i recently discovered your site… i made a few recipes and have not been disappointed yet- they are so simple to make- I made these muffins and took the cheesecake idea from your pumpkin cheesecake muffins and they were delicious- non Keto eaters approve of them- Keep the recipes coming- Thank you…
Can Adding sweetener affect consistency? Thanks
Do you mean more sweetener? That shouldn’t be a problem